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c_ .0

NOAA Estuary-of-the-Month
Seminar Series No. 6

r j

San Francisco Bayu^ *
Issues, Resources,
Status, and Management

October 1987

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

NOAA Estuarine Programs Office

^rC\ONAL

NOAA Estuary-of-the-Month
Seminar Series No. 6

San Francisco Bay:
Issues, Resources,
Status, and Management

Edited by David M. Goodrich

Proceedings of a Seminar
Held November 22, 1985
Washington, D.C.

U.S. DEPARTMENT OF COMMERCE

Clarence J. Brown, Acting Secretary

National Oceanic and Atmospheric Administration

J. Curtis Mack II, Acting Under Secretary

NOAA Estuarine Programs Office

Virginia K. Tippie, Director

Q f-l Sfe

\°i% 1

Si - Loj

San Francisco Bay

Environmental Status and Management
of Living Resources

an

ESTUARY-0 F-THE-MONTH
SEMINAR

presented
at the

U.S. Department of Commerce
14th & Constitution Avenue
Main Auditorium
Washington, DC

November 22, 1985

sponsored

by

THE NOAA ESTUARINE PROGRAMS OFFICE

and

THE U.S. ENVIRONMENTAL PROTECTION AGENCY

EDITORS PREFACE

The following are the proceedings of a seminar on San Fran¬
cisco Bay held on November 22, 1985, at the Herbert C. Hoover
Building of the U.S. Department of Commerce in Washington, D.C.
It was one of a continuing series of "Estuary-of-the-Month"
seminars sponsored by the NOAA Estuarine Programs Office (EPO),
held with the objective of bringing to public attention the
important research and management issues in our Nation's estu¬
aries. To this end, the seminar first presented an overview of
the Bay by senior scientific investigators, followed by an
examination of management issues by leaders of planning and
regulatory agencies involved in the Bay.

We would like to acknowledge the assistance of Dr. Michael
Josselyn of the Tiburon Center for Environmental Studies, San
Francisco State University, who had principal responsibility for
assembling the speakers. Dr. Josselyn's cooperation in produc¬
ing these proceedings and his experience with the Bay and its
people have been invaluable to us. The seminar series was or¬
ganized by Dr. James P. Thomas of the EPO, with the assistance
of other members of the EPO staff. Word processing for these
proceedings was done by Janet Davis.

David M. Goodrich

NOAA Estuarine Programs Office

Washington, D.C.

v

V

SAN FRANCISCO BAY

ISSUES. RESOURCES. STATUS, AND MANAGEMENT

Table of Contents

Page

Editor's Preface v

-David M. Goodrich

Congressional Views:

-Statement of Congressman Barbara Boxer 1

-Statement of Congressman Norman D. Shumway 3

-Statement of Congresswoman Sala Burton 7

Introduction to the San Francisco Bay Estuary 9

-Michael Josselyn

Estuarine Circulation and Mixing 21

-Roy A. Walters

Interannual Variability in Dissolved Inorganic 33

Nutrients in Northern San Francisco Bay Estuary
(abstract)

-David H. Peterson, Richard E. Smith,

Stephen W. Hagar, Dana D. Harmon,

Raynol E. Herndon, and Laurence E. Schemel

The Impact of Water Diversions on the River-Delta- 35

Estuary-Sea Ecosystems of San Francisco Bay
and the Sea of Azov

-Michael A. Rozengurt, Michael J. Herz
and Michael Josselyn

Thermal Dynamics of Estuarine Phytoplankton: 63

A Case Study of San Francisco Bay (abstract)

-James E. Cloern, Brian E. Cole,

Raymond L.J. Wong, and Andrea E. Alpine

Benthic Ecology and Heavy Metal Accumulation 65

-Frederic H. Nichols

Agency Cooperation and Fishery Studies
in San Francisco Bay
-Perry L. Herrgesell

69

77

The Impact of Estuarine Degradation and Chronic
Pollution on Populations of Anadromous Striped
Bass (Morone saxatilis) in the San Francisco
Bay-Delta, California: A Summary

-Jeannette A. Whipple, R. Bruce McFarlane,
Maxwell B. Eldridge, and Pete Benville, Jr.

Sublethal Effects of Contaminants on the Metabolism 107

of Metals and Organic Compounds in the Bay Mussel
-Florence L. Harrison and John P. Knezovich

Scientific Information and Management Policy for the 125

Delta-San Francisco Bay Ecosystem

-Michael J. Herz and Michael A. Rozengurt

Shoreline Management 137

-Alan R. Pendleton

The Federal Role in the Management of San Francisco Bay 149
-Betsy Coombs

California Regional Water Quality Control Board 155

San Francisco Region
-Roger B. James

vm

CONGRESSIONAL VIEWS:

STATEMENT OF CONGRESSWOMAN BARBARA BOXER

During my career as an elected official, I have always
served constituents who live on and around San Francisco Bay
and for whom the Bay is a symbol of environment values. During
these years, I have watched with alarm as Bay fill, pollution,
and water diversions contributed to the gradual decline of the
largest estuary on the West Coast, one of this country's most
valuable national resources.

Since coming to Congress two and one-half years ago, I have
sponsored legislation which would protect the Bay and adjacent
coastal waters, and I have fought to retain the National Marine
Fisheries Service Tiburon Laboratory and its critical research
on the effects of pollutants on striped bass and other fish. I
am a strong supporter of the Clean Water Act, especially the
amendment which would provide much needed funds for improved
information gathering and management of the Bay.

I am delighted the San Francisco Bay is the Estuary-of-the-
Month because such designation is an acknowledgement of concern
over the status of our Bay. NOAA's Estuarine Programs Office
and the EPA are performing an important public service by
bringing this excellent group of Bay researchers and managers
here to talk about the Bay's problems and by soliciting input on
solutions from Congress and other estuarine experts.

I look forward to an informative and productive day and I am
prepared to offer my support to assist in implementing any sug¬
gestions which are designed to enhance San Francisco Bay.

1

CONGRESSIONAL VIEWS:

STATEMENT OF CONGRESSMAN NORMAN D. SHUMWAY

I thought this morning I would like to focus my remarks on
three topics that are related to San Francisco Bay. One, of
course, is the coastal zone mechanism which California and the
Bay Area have developed to conquer problems in the San Francisco
Bay and ensure the success of that program. Secondly, is how
these programs begin to relate to activities outside of the
Bay's legal coastal zone. Thirdly, how the general experience
of the San Francisco Bay management can be used as an example
for other estuaries of national significance and more
specifically, what Congress has done recently.

Recognizing generally that there is a national interest in
the effective management, the beneficial use and protection, and
development of a coastal zone, Congress, in 1972, passed the
Coastal Zone Management Act (CZMA). The Federal program was set
up to encourage coastal states to develop their own individual
coastal management programs which accounted for national
interest and policies and to have these programs approved by the
Federal Government.

As you all may know, there are two basic incentives for a
coastal state to participate. These are, Federal funds to
coastal states to help develop and implement management
programs, and the consistency program which is a Federal
assurance that Federal activities directly effecting the coastal
zone will be provided to the maximum extent practicable and
consistent with approved state management programs. These two
incentives have been successful in getting 28 of the 35 coastal
states and territories to obtain Federally-approved management
programs. As a result of this achievement, the House of
Representatives, in June of this year, passed HR-2121 to
authorize Federal programs through the year 1990.

California has adopted a coastal zone management program and
incorporated a San Francisco Bay Plan into this program. Also,
as part of this program, an independent state agency was
created, the San Francisco Bay Conservation and Development
Commission, which we will refer to as BCDC. It is an agency
which is dedicated to the implementation of the Bay plan. All
of this, of course, is to achieve comprehensive bay management,
very fitting for the uniqueness of that resource.

In my mind, there are three significant advantages which the
CZMA lends to such an estuary management effort which guarantees
the success of the Bay plan's comprehensive approach, the
emphasis on state and regional responsibilities as the principal
managers, and the consultation ability which CZMA's consistency

3

provision provides. With regard to the first advantage, water
quality, recreational uses, air quality, shoreline growth, and
landslide activities are all related and should be managed as
such.

I think one of the aspects of the overall management of the
estuary would ensure a certain degree of inefficiency. For
example, as you probably know, early Federal efforts to manage
the Chesapeake Bay were largely ineffective because they
isolated only one aspect of estuarine management; in this case,
the Chesapeake Bay's water quality. Now, to combat that
approach, the EPA and the surrounding states are looking at the
factors involved in Chesapeake Bay water quality degradation.
They are looking at agricultural runoff, urban runoff, and other
landslide activities and not just at industrial sources. As a
result, we have a comprehensive approach which, I think all will
agree, is more effective than the initial approach.

With regard to the second advantage, it is most appropriate
that state, regional, and local officials be the principal
authors of any specific estuary management plan. The
appropriate rule under the CZMA is to provide limited grants to
assist in that effort, provide guidelines and technical
assistance relative to national interests, and to approve a plan
on development and implementation.

With regard to the third advantage, Federal consistency, in
the San Francisco Bay Plan has been implemented through a
consistency procedure and jurisdiction granted to the BCDC. The
relevant California state law, that is McAteer-Petris Act, has
been approved by NOAA pursuant to the CZMA, as part of
California's Federally-approved Coastal Management Program.

BCDC has authority over all areas of the Bay, extending
landward 100 feet, including Suisun Marsh and the surrounding
wetlands. Permits are required for practically all work
involving fill from the driving of a single pile to the
development of larger scale projects. Permits are issued only
if the proposed work is consistent with the McAteer-Petris Act
and the Bay Plan.

Let me give to you an example of what I think is good co¬
operation in the implementation of the Bay Plan. That is the
relationship of the U.S. Army Corps of Engineers and the BCDC.
Obviously, there are competing uses for the Bay and the shore¬
line. Probably the most critical has to be resolved in managing
the Bay. Since the Corps has permitting authority for all
proposals and the CZMA requires consistency certification for
such a Corps permit where activities are within the legal coast¬
al zone, the Corps simply recognizes a BCDC permit as a consis-

4

tency certification. With regard to jurisdiction, BCDC uses its
consistency authority to work with the appropriate local, state,
and Federal agencies conducting activities that could effect the
Bay.

For example, with regard to water quality matters, BCDC has
used this consistency provision as a comment authority on the
regional water quality award. Through their permitting process,
BCDC can actually enforce state water quality regulations. It
has been critical that BCDC and other effected agencies
recognize the legal limitation of the consistency provision.
Consistency should not be misconstrued as a state or local veto
over Federal matters, but rather as a mechanism designed to
promote state/ Federal consultation and resolutions wherever
practicable on matters of mutual or conflicting issues.

In Congressional activities relating to estuary management
in general, both the House and the Senate have passed legisla¬
tion to reauthorize the Clean Water Act. Included in both of
these bills are proposals for a National Estuary Program. These
proposals allow for a state governor to nominate estuaries which
are deemed to be of national significance to be included in this
program. If the EPA administrator concurs with that nomination,
a Congressional Committee is convened comprised of Federal,
state, and local officials to develop a water quality regulatory
program for those estuaries which have national significance.

Certain members of the Merchant Marine and Fisheries Com¬
mittee leadership, including Chairman Jones, are interested in
broadening the scope of these programs and shifting their focus
to develop an overall management program as opposed to programs
specifically limited to water quality. These broad regulatory
programs will then be forwarded to the state CZMA plan.

I believe there is some merit in this Merchant Marine and
Fisheries Committee approach. Certainly, the more comprehensive
the management framework and more of the state and local role in
estuarine programming is increased, the more appropriate and
effective, I believe, the management will be.

However, as we have seen in the case of the San Francisco
Bay, the Federal mechanism in the form of CZMA is already in
place. I believe it promotes a comprehensive estuary management
regime.

We are seeking ways to cut Federal spending. Reduction
mechanisms are being seriously considered by Congress. I think
it is going to be hard to justify a new program for management
of estuaries, even those that have national significance. I
believe that maybe a more appropriate method of encouraging

5

states to use the CZMA will be simply to amend the 1977 Act to
outline national interests for specific management plans for
estuaries of national significance as part of the Federally ap¬
proved coastal management programs, as San Francisco, I believe,
has already done.

The San Francisco Bay has provided examples. Example 1 is
that CZMA worked. Example 2 is that it has influence, which
certainly effected its own strength and legal confines and is
felt in surrounding areas as well. I think it also provides
comprehensive and overall management to a resource which is
valuable to all of us as Americans and certainly to those of us
who are Californians.

Obviously, Congress does not yet have answers to all the
challenges that we face. I think we are going to be looking to
people such as you to provide recommendations and guidance for
our actions and activities in the future. I look forward to
that kind of product coming from you and from this conference
and I look forward to working with you in the months and years
ahead. Thank you.

6

CONGRESSIONAL VIEWS:

STATEMENT OF CONGRESSWOMAN SALA BURTON

Estuaries in the surrounding California marshes and life
carrying tributaries are unique ecosystems of great value to man
and nature. Yet, for too long, estuaries have been regarded as
useless resevoirs for municipal and industrial waste.

More than 100 acres of estuarine habitat have been lost
nationwide since 1960 and estuaries around the country have been
considered ecologically. One of those estuaries is of great
concern to me and happens to be the largest estuary on the West
Coast, San Francisco Bay, and it's in serious trouble. The
striped bass population has plummeted 80 percent in the past two
decades. Salmon, trout, shad, and crab populations have also
seriously declined. High concentrations of toxics have been
found in the Bay and is the highest ever recorded in scientific
literature. Ninety-five percent of the Bay's original wetlands
have been converted to non-wetland use depriving the Bay of re¬
quired pollution filtration and wildlife habitat functions. In
fact, this is a matter I have addressed with the Army Corps of
Engineers in hope that greater attention will be given to these
concerns that are so important to the continued health of the
Bay.

As you may be aware, I have offered an amendment to the
Clean Water Act legislation, HR-8, which authorizes development
of the San Francisco Bay estuarine programming. Since San Fran¬
cisco Bay estuarine watershed is the coastal line to the State
of California, the Bay system does not currently qualify under
the interstate provision of the national program. The intent of
this amendment is to develop a management plan for the Bay's
estuaries which would be similar to the national plan indicated
under the EPA's estuary program authorized by Section 320 of the
Clean Water Act. HR-8 has passed the House with this amendment
in tact but the Senate has not included this language in its
Clean Water Act. A conference between the House and the Senate
is expected to convene after the Thanksgiving recess to rectify
the differences in these bills. We are working very hard to
make sure that San Francisco Bay is included in the final ver¬
sion.

I am very pleased that this seminar is being held to discuss
San Francisco Bay and I want to thank you for permitting me to
speak on this most important issue for San Francisco. Thank
you.

7

INTRODUCTION TO THE SAN FRANCISCO BAY ESTUARY

Michael Josselyn

Paul F. Romberg Tiburon Center for Environmental Studies
San Francisco State University

It is a pleasure to welcome our audience to a day-long
presentation on San Francisco Bay, our Nation's second largest
estuary and perhaps also its youngest in terms of scientific
research and understanding. As we shall hear today, San
Francisco Bay is a key region in the management of California's
water, and we greatly appreciate the Congressional interest
given to this important national resource. Currently, the House
of Representatives has passed an amendment to the Clean Water
Act which designates a greater role for the U.S. Environmental
Protection Agency in managing our Nation's estuaries, and we
look forward to working with Congress to ensure the San
Francisco Bay estuary is included in that effort.

Before I begin my introduction to the San Francisco Bay
estuary, I would like to acknowledge the support and assistance
provided by Dr. James Thomas, Acting Director, and the staff of
the Estuarine Programs Office. We are pleased to be the sixth
in what is an excellent series of seminars on the Nation's
estuaries. In addition, I wish to acknowledge the support of
the agencies of the individual speakers, especially the U.S.
Geological Survey, the National Marine Fisheries Service, and
the Environmental Protection Agency, Region 9.

My role is to set the stage for the following speakers.

Many of the audience may have seen the San Francisco Bay region
previously; others may have only limited knowledge of its
history, geomorphology, and the problems. We, as estuarine
scientists, are not as fortunate as our colleagues along the
eastern and Gulf coasts of the United States, in that large
estuaries are a rare phenomena along the precipitous coastline
of the western United States. More typical are small coastal
rivers and streams entering the ocean over sand bars with narrow
coastals marshes behind the dunes. Larger rivers such as the
Columbia support more extensive estuarine habitats within the
confines of the river valley. However, only in a few areas have
the coastal mountains opened to a broad semi-enclosed basin
which supports typical habitats associated with the estuaries
environment: tidal marshes, mudflats, and protected open

water. Coupled with the freshwater inflow from the Sacramento
and San Joaquin Rivers, the San Francisco Bay basin provides a
unique physical environment which supports a great number of

9

organisms tolerant of fluctuating salinities, temperature, and
turbidity. Some of the geophysical facts about San Francisco
Bay and its comparisons with other estuaries are given in Tables
1 and 2.

Although estuaries have many qualities and functions in
common, the San Francisco Bay estuary has many distinctive
attributes compared to other estuaries in the United States.

The estuary is actually a continuum of basins, deltas, and
rivers -- as my fellow scientists at the Romberg Tiburon Center,
Dr. Michael Rosengurt, refers to as the River- Delta-Estuary-Sea
system. Two major rivers flow into the basin: the Sacramento
and the San Joaquin. Together, they drain over 40 percent of
the State of California (approximately 153,000 km2). Before
reaching the estuarine portion of the basin (where salt and
freshwater mix), the two major rivers mix with other tributaries
with a vast interconnecting maze of channels called the Sacra-
mento-San Joaquin Delta (Figure 1). The Delta, once the largest
(over 1,400 km2), is now largely used for farming and recre¬
ation. As our speakers will relate, the Delta also represents
the single most important element in the vast "pipe-work" of
water conveyance facilities in the state as well as providing
important spawning and nursery areas for the state's
recreational fisheries.

Although many estuaries have variable inflow rates associat¬
ed with storms and snowmelt, the annual inflow pattern to the
San Francisco Bay estuary fluctuates in response to the Mediter¬
ranean-type climate: frequent and heavy winter storms followed
by dry summers. Winter rains result in both immediate local
runoff and accumulation of water in the snow pack, which later
melts and results in heavy discharges in April and May. With an
approximate annual river discharge of 20.9 x 102 m3, 80-90
percent enters the estuary from December to April (Figure 2).

The climate also affects net water budgets due to the greater
amounts of evaporation occurring in the region evolution of a
unique marsh ecosystem, sometimes referred to in creation of a
major business for salt production in large evaporation ponds.

For those of you who have flown into San Francisco Bay, these
large multi-hued basins are often the most distinctive landform
on the approach path.

Another unique characteristic of the San Francisco Bay
estuary is the separation of the basin into two major circula¬
tory systems. The "North Bay", consisting of Suisan, San Pablo,
and the northern portion of San Francisco Bay (sometimes re¬
ferred to as the "Central Bay") is dominated by a typical estu¬
arine gravitational circulation pattern. Freshwater inflow
meets the bottom-flowing oceanic water in the region between
Chipps Island in the western Delta and San Pablo Bay depending
upon the amount of inflow. During the summer, the usual loca¬
tion of this interface region is within Suisun Bay, where it is

10

Figure 1. Map of San Francisco Bay
Delta region, the North Bay and the

showing the
South Bay .

11

16

Figure 2. Interannual variation in
freshwater inflow to San Francisco Bay
es tuary .

A. Regulated freshwater inflow as
measured in the Delta

B. Salinity change as measured in
the Central Bay. From Conomos
et al^ (1985)

Figure 3. Annual water budget for the
San Francisco Bay region. The region
exhibits a net evaporative loss over
the year with rainfall confined to the
winter months. From Conomos et al. (1985)

12

Table 1

Comparisons of San Francisco Bay
with Other North American Estuaries

Basin Area

Surface Area

Inflow

(1000 km2)

(km2)

(m3/s)

San Francisco Bay

153

1240

500

Columbia River

671

380

5500

Fraser River

203

-

2700

Delaware Bay

33

303

550

Chesapeake Bay

166

11400

1600

From Conomos et al. (1985)

Statistic

Table 2

Geostatistics of San Francisco Bay

Value (x 1C)9)

Area (mean lower low water)

1.04 m

Including mud flats

1.24 m

Volume

6.66 m

Tidal Prism

1.59 m

Average Depth

6.1 m

Median Depth

2.0 m

Regulated River discharge (annual)
Delta outflow

19.0 m3

All other streams

1.9 m3

2

2

3

3

Modified From Conomos et al. (1985)

13

referred to as the null zone and has been shown to support a
significant phytoplankton- zooplankton food web. On the other
hand, the "South Bay", the portion stretching from the indus¬
trial city of South San Francisco to the Silicon Valley of San
Jose, has little freshwater inflow and functions more like a
large lagoon. Occasional freshwater cells may move into the
basin from the North Bay during the winter. In the summer, the
major freshwater source is treated domestic effluent.

The Urbanized Estuary

Flying into San Francisco or viewing the region from space,
one is impressed with the urban development surrounding the Bay.
Certainly, the land-use along the edge of the Bay has undergone
a significant change over the past 170 years; these changes un¬
doubtedly have had an influence on the physical, chemical, and
biological functioning of the estuary. Nichols et al. (1986)
have written an excellent summary of the changes that have oc¬
curred in San Francisco Bay since 1850 and I want to briefly
summarized their remarks.

One of the major activities was the diking of "swamp and
overflowed lands" and subsequent draining of the wetlands for
agricultural purposes. The greatest loss occurred in the Delta,
where the entire wetland system was lost due to the construction
of levees. Small portions of the wetland system can be observed
today as islets within the river channels and along levee banks.
However, the increasing trend towards placing a rip-rap on le¬
vees and removing vegetation is eliminating even these small
riparian areas. The tidal salt marshes of the Bay have faired
only slightly better, with over 85 percent having been diked or
filled for agricultural, salt, ponds, or urbanization. The
largest remaining wetland system in the estuary is located
around Suisun Bay. These wetlands are also diked; however,
water flow is managed to support habitat to attract waterfowl
for hunting by the over 150 private duck clubs in the region.

At the time that wetlands were being diked, another anthro¬
pogenic process was imperceptibly building more shallow water
habitat. To retrieve gold from the foothills, miners used large
water monitors to wash the overburden and gold-containing sedi¬
ment through sluiceways and into rivers, the Delta and, after
several decades, the Bay. Hydraulic mining was halted in 1884,
but the redistribution of sediment from rivers to the Bay went
on for the following half century. In several locations in
Suisun and San Pablo Bays, new marshlands were created by the
sediment, and many former deep harbors were silted in.

The gold of California transplanted many Easterners to the
Bay region, who brought with them the cultural and culinary
tastes of their Atlantic upbringing. With the completion of the
transcontinental railroad, the means to transport entire

14

estuarine communities (with the purpose of introducing the
eastern oyster) became available. Oyster culture in San Fran¬
cisco Bay was a major industry, and with it came other mudflat
organisms. Some were edible, some innocuous, several destruc¬
tive (e.g. Teredo, the shipworm) . All were aggressive and
quickly became dominant members of the Bay's fauna. Today, over
100 species of introduced benthic and intertidal invertebrates
are found in the Bay as well as fish, plants, and zooplankton.

One of the most popular introduced species is the striped bass
which, as will be described by Dr. Whipple later this morning,
has also become the Bay's "miner canary" in that its recent
decline may be a warning of a system pushed beyond its natural
resilience.

While the marshes were being filled and new species
introduced, another activity began in the Central Valley and
southern California which would have an impact on the Bay --
irrigated agriculture. The demand for water for the arid south
brought political and economic pressures for state and Federal
water projects to redirect water from the Bay to other uses.
Although water flow varies considerably from year-to-year, the
loss of freshwater inflows is evident, amounting to 40-60
percent of the natural flows in recent years (see Rozengurt,
this proceedings). Much of the diverted water is taken from the
spring flows, an important period for some spawning fish.
Furthermore, the water from Sacramento Valley (which receives 7 0
percent of the state's runoff) must pass through the strategi¬
cally located Delta before reaching the pumping facilities at
Tracy. The Delta is not only an important fish habitat, it also
affects downstream salinity intrusion, sedimentation, and
flooding. Yet this "sieve", through which freshwater must pass,
is itself weakening as increasingly, frequent levee failures
during floods and winter storms occur.

The discussion of water needs and natural resource require¬
ments is always bound to create an argument among farmers, bio¬
logists, and public interest groups. Even the Federal and state
authorities responsible for separate water storage and convey¬
ance facilities had no joint operating agreements until 1986.

The State Water Quality Control Board issued a policy (referred
to as Decision 1485) to provide for water flows necessary to pro¬
tect the beneficial uses of the Delta; the decision is up for
renewal in 1988. We can expect a great deal of data, interpre¬
tation, and emotion at these hearings given the impact such a
decision can have on the competing demands for water use for
economic and natural resource protection purposes.

The reduction in water quantity has been accompanied by a
reduction in water quality. Fortunately, San Francisco Bay
recovered from the anoxic events of the 1950s and 1960s as a
result of improved wastewater treatment and the movement of
discharge locations to regions of greater flushing. Yet

15

population growth has expanded the amount of effluent entering
the Bay such that the ratio of wastewater to freshwater inflow
is expected to double by the year 2000. As our technology to
treat domestic effluent has increased, so has our society's
ability to produce more toxic materials as both agricultural and
industrial waste. Some of the highest concentrations of DDT and
heavy metals among the world's estuaries have been observed in
the sediments of San Francisco Bay. Organic compounds such as
PCBs and PAHs are also found in Bay organisms and in some cases
have been implicated in reproductive failure.

People visiting the Bay area are sometimes tempted to
question the impacts of the problems presented this morning.

The sun rising over wispy fog and blue water presents a wonder¬
ful view to the visitor perched on the hills overlooking the
Bay. The striped bass fisherman, the avid bird watcher, the
beachcomber seeking shellfish in the mudflats, and the beachgoer
during summer months, each suffer a small loss of quality in the
Bay resources. They combine to represent a powerful environ¬
mental lobby to protect one of California's most important
natural resources.

The Scientific Perspective

The primary purpose of our seminar is to describe the state
of our scientific information concerning San Francisco Bay.
Luckily, I've brought with me individuals far more knowledgeable
about that topic that I, and I only want to briefly refer to the
landmarks and "bibles" on San Francisco Bay ecology.

The early history of discovery and scientific exploration of
the Bay has been eloquently described by Joel Hedgepeth (1979).
Science as politics has its backrooms, and Dr. Hedgepeth manages
to find enough old letters and documents to indict even the
staid old institutions of Stanford and the University of
California in a battle over scientific territory. Not only
scientists, but vaudeville actors like John Reber have played a
role in stimulating research interest in the estuary. Mr.

Reber's desire to convert the Bay into a large freshwater re¬
servoir provided the impetus to construct the Corps of Engineers
Hydraulic Model, which has tested Mr. Reber's plan as well as
many others. A number of Bay-wide studies have been undertaken
but unfortunately, differences in methodology and changes in our
understanding of the underlying physical and geological pro¬
cesses have limited the usefulness of this store of information.

This level of effort has yielded a number of significant
volumes which should be read by all scientists and managers
responsible for determining the future of research and manage¬
ment of the Bay. In 1977, the Pacific Section of the American
Association for the Advancement of Science held a conference at
San Francisco State University on San Francisco Bay and in 1979,

16

published a volume entitled San Francisco Bay: The Urbanized
Estuary (Conomos, 1979). This excellent work brings together
much of the recent work done by the U.S. Geological Survey
personnel on estuarine circulation, chemistry, and biology. It
also provides summaries of general geomorphology of the estuary,
wetland geology and biology, and fisheries resources. A less
successful volume followed in 1982 as an outgrowth of another
Pacific Section-sponsored symposium at the University of Califor¬
nia at Davis (Conomos et al. 1982). Entitled San Francisco
Bay: Use and Protection, this book discusses impacts of shore¬

line development, sewage treatment, water diversion, and dredg¬
ing on the estuary. The U.S. Fish and Wildlife Service, in its
community profile series, sponsored the completion of a profile
of tidal marshes in San Francisco in 1983 (Josselyn, 1983) and
has now contracted for profiles on freshwater tidal marshes and
the soft-bottom benthos.

The most recent addition to this list of scientific litera¬
ture is the book edited by Cloern and Nichols (1985). The pur¬
pose of the volume is "to examine the temporal dynamics of [estu¬
arine] properties and processes in the San Francisco Bay es¬
tuary", in which "temporal" is defined as time scales from tidal
to interannual. It provides updated information from the U.S.
Geological Survey work as well as research sponsored by the U.S.
Bureau of Reclamation, California Department of Fish and Game,
and California Water Resources Center. In the volume, both the
individual authors and the editors comment on the areas needing
further research.

Areas of Recommended Research Effort

As I prepared for this presentation, I contacted a number of
individuals who have or are currently involved in research on
San Francisco Bay. Most agreed that the work mentioned above
has provided a sound framework for more detailed scientific
efforts. It is apparent from the efforts of the U.S. Geological
Survey and the Four Agencies Ecological Study Program (a group
comprised of the Department of Fish and Game, Department of
Water Resources, State Water Quality Control Board and the
Bureau of Reclamation) that large scale coordinated programs
have yielded significant data linking physical, chemical, and
biological processes. At the same time, individual research on
specific groups or hydrologic cycles has also yielded important
new information on the estuary. Both levels of effort are
needed. Table 3 indicates some of the major research needs as
summarized by Cloern and Nichols (1985) with some additions as
suggested by my colleagues.

Research of itself has led to major breakthroughs in our
understanding of estuarine processes. At the same time, the
urbanized nature of San Francisco Bay estuary requires that we
use this research to solve immediate management needs. The next

17

Table 3

Research Priorities for the San Francisco Bay Estuary

ROLE OF INFLOW ON ESTUARINE PROCESSES

Circulation and residence times
Salt balance

Sedimentation and transport
Geochemical cycles
Fisheries resources

BIOLOGICAL PROCESSES

Microbial ecology

Micozooplankton biology

Role of seasonal and tidal wetlands

Benthic vegetation: eelgrass and algae

Scale of temporal variability in biotic communities

WATER QUALITY

Long-term monitoring of biotic communities
Sources and fates of toxics

Development of new techniques to measure impacts of
toxics

Nutrient budgets for the estuary

Table 4

Major Management Issues for San Francisco Bay

Freshwater diversion from Delta and Bay*

Toxic waste discharge to ground and surface waters*
Agricultural drainage
Loss of wetlands*

Decline of fisheries

Sea level rise

Dredging to deepen channels

*Signifies those issues of high significance.

18

several decades will bring significant new stresses on the
estuarine system which will equal, if not exceed the historic
human impacts on the region. Table 4 provides a short list of
these management needs.

REFERENCES

Cloern, J.E. and F.H. Nichols, 1985: Time scales and mechanisms
of estuarine variability, a synthesis from studies of San
Francisco Bay. In Cloern, J.E. and F.H. Nichols (eds.).
Temporal Dynamics of an Estuary San Francisco Bay. D.W.
Junk Publishers, Dordrecht, The Netherlands.

Conomos, T.J., R.E . Smith and J.W. Gartner, 1985: Environmental
setting of San Francisco Bay. In Cloern, J.E. and F.H.
Nichols (eds.). Temporal Dynamics of an Estuary: San
Francisco Bay. D.W. Junk Publishers, Dordrecht, The
Netherlands.

Hedgepeth, J.W., 1979: San Francisco Bay: The unsuspected
estuary. In Conomos, T.J. (ed.). San Francisco Bay: The
Urbanized Estuary. Pacific Div. AAAS , San Francisco, Ca.

Josselyn, M.N., 1983: The Ecology of San Francisco Bay Tidal
Marshes: A Community Profile. U.S. Fish and Wildlife

Service, U.S. Department of the Interior, Report No.
FWS/OBS-83/23.

Nichols, F.H., J.E. Cloern, S.N. Luoma, and D.H. Peterson,

1986: The modification of an estuary. Science 231:567-573.

19

ESTUARINE CIRCULATION AND MIXING

Roy A. Walters
U.S . Geological Survey

Abstract

Tidal-period and low-frequency variations in sea level,
currents, and mixing processes in the northern and southern
reaches of San Francisco Bay lead to contrasting characteristics
and dissimilar processes and rates in these embayments; the
northern reach is a partially mixed estuary whereas the southern
reach (South Bay) is a tidally oscillating lagoon (tributary
estuary) with density-driven exchange with the northern reach.

The mixed semidiurnal tides are mixtures of progressive and
standing waves. The relatively simple oscillations in South Bay
are nearly standing waves, with energy propagating down the
channels and dispersing into the broad shoal areas. The tides
of the northern reach have the general properties of a progres¬
sive wave but are altered at the constrictions between embay¬
ments and gradually change in an upstream direction to a mixture
of progressive and standing waves. The spring and neap varia¬
tions of the tides are pronounced and cause fortnightly varying
tidal currents that affect mixing and salinity stratification in
the water column.

Wind stress on the water surface, freshwater inflow, and
tidal currents interacting with the complex Bay topography are
the major local forcing mechanisms creating low-frequency
variations in sea level and currents. These local forcing
mechanisms drive the residual flows that, with tidal diffusion,
control the water replacement rates in the estuary. In the
northern reach, the longitudinal density gradient drives an
estuarine circulation in the channels, and the spatial variation
in tidal amplitude creates a tidally-driven residual circu¬
lation. In contrast, South Bay exhibits a balance between wind-
driven circulation and tidally-driven residual circulation for
most of the year. During winter, however, there can be suffi¬
cient density variations to drive multilayer (2 to 3) flows in
the channel of South Bay.

Residence times of the water masses vary seasonally and
differ between reaches. In the northern reach, residence times
are on the order of days for high winter river discharge and of

21

Figure 1.

Index Map

22

months for summer periods. The residence times for South Bay
are fairly long (on the order of several months) during summer,
and typically shorter (less than a month) during winter when
density-driven exchanges occur.

The subject that I would like to deal with is circulation
and mixing in the San Francisco Bay estuary. From an overall
perspective, perhaps, the physics of an estuary is not quite as
glamorous as the chemistry and biology. Nonetheless, it is a
very necessary foundation on which distributions in chemistry
and biology rest.

The U.S. Geological Survey initially became involved in
studies of San Francisco Bay in approximately 1969 through
investigations in marine geology. They did one of the first
things to study water movements; that is, they dropped a bunch
of drifters into the Bay to see where they would go. Immedi¬
ately, they were involved in controversy because their findings
had impact upon possible water deliveries by the California and
Federal water projects. Since those controversial beginnings,
we have expanded into a comprehensive research group studying
aspects of the physics, chemistry, and biology of San Francisco
Bay.

What I would like to do now is take you through the present
understandings of the circulation and mixing in the estuary.

In the beginning, there was the Ice Age, which had direct
implications for San Francisco Bay. The most notable thing was
that water held as ice led to the lowering of sea level by as
much as 100 meters or so. At this time, the Bay was a river
plain, cut by several river channels. As sea level rose, the
drowned river valley became t:he Bay and the relict river chan¬
nels became the shipping lanes.

What I would like to bring to your attention in Figure 1 is
the deepest part of the Bay. You will see immediately that
there is a channel that comes entirely down the northern reach
of the Bay and out through the Golden Gate. There is also a
channel that starts in the southern end and goes out through the
opening at the Golden Gate. These are relict river channels.

Most of the freshwater flow comes down the northern reach --
about 90 percent of the total flow into the Bay. The channel
left from the last ice age made this area; this area was dry at
one time. The ocean shore was out past the Golden Gate on the
continental shelf.

The shoals contrast with the rest of the Bay. The depth is
of the order of a few meters in the shoals and up to 10-15 met¬
ers in the channel, except near the Golden Gate where the depth
is about 100 meters.

The bathymetry has a profound affect on the circulation and
mixing. High current speed tends to occur where the water is

23

deep, whereas mixing increases with current speed and with de¬
crease in depth.

Next, I'd like to talk about the actual physical processes
that drive the circulation. These include the inflow of fresh¬
water, the propagation of tides, and other sea level variations
through the Bay, and wind stress on the water surface. The
first, the one with the greatest controversy, is the amount of
freshwater inflow into the upper end of the Bay. At the seaward
boundary there is saltwater, which is relatively dense, ap¬
proximately 2 percent heavier than freshwater. By contrast,
there is freshwater introduced through the Delta, in through
Suisun Bay, down through San Pablo Bay, and out through the
Golden Gate. A good conceptual model of this system is one of a
partially mixed estuary; that is, salt and freshwater mixed in a
continuous manner from the Delta down through the Golden Gate in
the northern reach. South Bay is what is called a tributary
estuary, that is, like an appendage hanging on to the main
estuary. In fact, the main estuary determines the type of
circulations and exchanges that go on there. This is very
similar to the Chesapeake, for instance. Chesapeake Bay is the
main stem and there are the tributary estuaries such as the
Potomac.

The second physical forcing process is the sea level changes
at Golden Gate. It's important to separate different time
scales when you're talking about sea level changes.

San Francisco Bay, unlike East Coast estuaries, is very much
dominated by tides. If you were to measure sea level and call
that the signal, you would find that approximately 95 percent of
that signal is the tide. The system is essentially dominated by
tides. But the tides go roaring in and the tides go roaring out
leaving a small average circulation. This little difference is
what is important to the long-term effects, that is, seasonal
patterns and the way the biology responds over the seasonal
cycles.

So we can consider sea level to be broken into two frequency
ranges. One is the tidal period variations, which we'll dispose
of shortly. The other is what we call the low frequency or
subtidal variations. Now, in perspective, this would include,
for example, the 10-day period in the weather that blows up and
down the coast of California on the continental shelf. It would
involve storms passing through the system, setting up sea level
and causing sea level changes. It also can be related to the
local rise of sea level.

The third forcing function we should talk about is the wind
stress on the water surface. We have considered the seaward
boundary condition, mainly sea level, and the landward boundary
condition, namely the input of freshwater. We must now examine
the surface boundary condition, the wind stress.

The winds in San Francisco Bay, at least in the summer, are
characterized by very strong diurnal variations; that is, a
land/sea breeze that is driven by the temperature difference
between the land and the sea. During the winter, when storms
come through, this whole pattern is upset, and there are very
strong winds from the southwest and sometimes from the north¬
west. This has a tendency to create perturbations in the cir¬
culation, after which time it returns to a more steady rate.

Let's talk in more detail about tides. The variations in
sea level at the Golden Gate create a tidal wave which propa¬
gates into the Bay. The tidal characteristics between the north
and south ends of the Bay are quite different. The south end of
the Bay has what one would call a standing wave; that is, as you
look at the windward side of a fixed object in the water, you
would see a reflected wave and an incident wave. These two
waves propagate against each other, creating a standing wave.

Now, one characteristic of a standing wave is that the maximum
velocities occur when the tide is in the midpoint between its
extreme.

The characteristics of the tide in the northern region is a
combination of a standing and a progressive wave; that is, the
current speed is maximum at the crests and troughs, like wind
waves on a lake. There is quite a phase lag as the wave propa¬
gates up the reach, perhaps three or four hours before it comes
to Suisun Bay.

Sea level is, of course, continuous across central San
Francisco Bay. However, the water currents have a different
phasing as you traverse the central bay area. What you find is
that the tide turns first in South Bay and then later in the
northern reach. For instance, when the tide turns and starts to
flood, it will change first and start flooding in South Bay be¬
cause it changes at the mid-tide level, whereas it's not going
to change in the northern part until several hours later. Water
flows out to the northern reach, into the South Bay, while the
water is starting to flood into Golden Gate. Eventually, the
water will turn and start propagating up the northern reach.

What you have is an unusual but very effective way to pump water
between the north and south reach of the Bay.

Looking at the tides as they propagate through the Bay from
the Golden Gate, you can see, if you look at tidal amplitudes,
that the amplitude of the wave is increased as it goes south,
which is a characteristic of a standing wave. Phase differences
here are small, that is, everything happens simultaneously. In
the northern reach, there is a tendency for local reflections to
occur, for example, at the eastern end of San Pablo Bay. In
fact, the phase increases in a monotonic manner up the northern
reach. The tidal currents in San Francisco Bay are quite large.
At Golden Gate, there is a constriction, leading to currents of
up to 5 knots.

25

Next consider the salinity distribution. The largest
freshwater inflows occur in winter and spring. The lowest
salinity occurs in the upper end of the estuary, in the northern
reach. You can see this in Figure 2. The first contour on the
right is for two parts per thousand. You can see salinity is
depressed into San Pablo Bay, due to the high freshwater in¬
flow. In this case, Suisun Bay is becoming more like a river
than an estuary.

The salinity near Golden Gate is depressed slightly while
that in South Bay remains fairly high, again attesting to the
fact that there is little freshwater inflow into South Bay.
Typically in summer, you will find that the salinities are very
much raised in the upper estuary because of the reduction of the
freshwater inflow.

I'm going to start at the north end of the estuary, Suisun
Bay, and come down to Golden Gate, giving an overview of the
circulation, and then touch upon South Bay. In the upper end of
the estuary, Suisun Bay, the river input comes from the Delta,
the confluence of the Sacramento and San Joaquin Rivers. As the
rivers comes out through Suisun Bay, you can see the sediment
pattern as it flows out between the islands and passes the
reserve fleet on the northwest shore.

There are two types of circulation. One is a horizontal
circulation pattern that is more or less uniform in depth and is
driven by the freshwater flows and by tidal effects. Then in
the vertical, there is a circulation with dense saltwater
intruding on the bottom and freshwater flowing out on the
surface. This is called estuarine circulation. Each of the
different kinds of circulation causes a different kind of
mixing. In the case of Suisun Bay, there is a net outflow due
to freshwater inflow. Because of the small residual tidal
effect, there is also a net counterclockwise circulation,
through the islands and up the main channel. And because of the
estuarine circulation, there are also density currents coming up
the channel. Figure 3 is a schematic representation of how the
currents flow. Look in particular at the one called "water
flow". What you can see is the river coming in from the left,
more or less uniformly with the depth, while the saltwater flows
from the ocean on the bottom. There is a mixing zone, which
usually occurs somewhere in Suisun Bay. There is some mixture
of this fresh- and saltwater which then flows out as a surface
layer. In San Francisco Bay, because there's so much tidal
energy, the water column is well mixed in the vertical. There
is a horizontal decrease in salinity going up estuary, and you
still see an estuarine circulation.

26

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27

WATER

WATER

DENSITY

FLOW

*<‘o-***

Figure 3. Schematic of a
the ocean water on the ri
on the left. There is a
ocean flowing up-estuary
compensating return flo w
from Cloern, 1979.

density current with
ght and freshwater inflow
density current from the
on the bottom and a
at the surface. Modified

28

1982

Figure 4. A time series of (A) residual velocity
(U is the longitudinal component, positive up estuary) ,
(B) salinity and (C) salt flux components at a current
meter station south of San Bruno Shoal in South Bay.

The current peak around February 16 depicts a density
current inflow into South Bay during neap tides. Note
also the rise in salinity and the peak in salt flux
at the time. From Walters et al. , 1985

29

The horizontal circulation is in fact a very effective
mixing mechanism. The point I want to bring out is that mixing
is very complicated, much more complicated than most East Coast
estuaries. When you anticipate or plan modifications in the
estuary, it is really difficult to say with any certainty what
is going to happen in more than a qualitative sense.

We skipped over San Pablo Bay, which is very similar to
Suisun Bay in that there is still a large horizontal, rotating
residual current. There are the outflowing currents which occur
at the surface in the channel. There are density currents going
up the channel. But the density currents are interesting in San
Pablo Bay, and they're very similar to those in South Bay. So
I'll point to this example.

One of the important features here is the shoal area in the
center of the channel in San Pablo Bay. The density currents
that come into the Bay are stronger where the water is deeper.
This density current moves up through the northern reach of the
Bay. Because the water is so shallow in the center of San Pablo
Bay, it can't really sustain this density current. What in fact
happens is that the density current more or less vanishes on the
shoal, and then re-forms on the other side of the shoal toward
Carquinez Strait.

It's really an interesting feature. You might ask yourself
how the salt is getting past the shoal. Apparently, it's doing
this by tidal pumping. That is, on the flooding tide, saline
water flows over the shoal, into the channel. On the ebb, less
saline surface water flows out over the shoal. So there is a
tidally induced exchange over the shoal.

In South Bay, something very similar occurs. Because South
Bay is a tributary estuary with little freshwater inflow, the
freshwater has to come from the north end, from Central Bay.

For most of the year, South Bay is at oceanic salinity. It's
just sitting there equilibrated with Central Bay.

During winter, with the big freshwater flows coming down
from the northern reach, the salinity in Central Bay is de¬
pressed and the water in South Bay then drains out as a density
current. When freshwater inflows decrease, the salinity starts
to go up in Central Bay; the water in Central Bay then drives
back into South Bay as a density current in the opposite direc¬
tion. There is again the dispersion mechanism of tidal pumping
over the shoal.

In fact, +*hat is the big event of the year in South Bay,
especir-'.^y for mixing. Figure 4 depicts this. After freshwater
inflow peaks and South Bay salinity is increasing, there is a
density current being driven into the channel. But because of
the tide, when there are spring tides, there's a lot of vertical
mixing, and the currents are very sluggish and slow. During
neap tides, when the tidal energy is low, there is less vertical
mixing and the density currents really pick up speed. You can

30

see in the top picture, there is a very strong density current
occurring over the shoal. There is, in this case, mid-level
outflow similar to that occurring in Baltimore Harbor.

I'll just say in closing that we are riding a new wave of
understanding. One of the most important recent events in the
studies of San Francisco Bay was when NOAA/National Ocean
Service, with cooperation from USGS, did a sea level and current
meter survey in 1980. We're at the point now where we're fully
involved in the interpretation of this data set. For those
people interested in further information, we have recently
prepared an article summarizing the current state of under¬
standing of circulation and mixing in San Francisco Bay (Walters
et. al. 1985).

REFERENCES

Cloern, J.E., 1979: Phytoplankton ecology of the San Francisco
Bay system: The status of our current understanding, in
T.J. Conomos (ed.), San Francisco Bay: The Urbanized
Estuary. Pacific Division, American Association for the
Advancement of Science, San Francisco, Ca. 64-72.

Conomos, T.J., 1979: Properties and circulation of San Fran¬
cisco Bay waters, in T.J. Conomos (ed.), San Francisco Bay:
The Urbanized Estuary. Pacific Division, American Associa¬
tion for the Advancement of Science, San Francisco, Ca.
38-50.

Walters, R.A., R.T. Cheng, and T.J. Conomos, 1985: Time scales
of circulation and mixing processes of San Francisco Bay
waters. Hvdrobioloaia 129:13-36.

31

INTERANNUAL VARIABILITY IN DISSOLVED INORGANIC NUTRIENTS

IN NORTHERN SAN FRANCISCO BAY ESTUARY

David H. Peterson, Richard E. Smith, Stephen W. Hagar,
Dana D. Harmon, Raynol E. Herndon, and Laurence E. Schemel

U.S. Geological Survey

Abstract

Nearly two decades of seasonal dissolved inorganic nutrient-
salinity distributions in northern San Francisco Bay estuary
(1940-1980) illustrate interannual variations in effects of
river flow (a nutrient source) and phytoplankton productivity (a
nutrient sink). During winter, nutrient sources dominate the
nutrient- salinity distribution patterns (nutrients are at or
exceed conservative mixing concentrations). During summer,
however, the sources and sinks are in close competition. In
summer of wet years, the effects of increased river flow often
dominate the nutrient distributions (nutrients are at or exceed
conservative mixing concentrations), whereas in summers of dry
years, phytoplankton productivity dominates (the very dry years
1976-1977 were an exception for reasons not yet clearly known).
Such source/sink effects also vary with chemical species.

During summer, the control of phytoplankton on nutrient distri¬
butions is apparently strongest for ammonium, less so for
nitrate and silica, and is the least for phosphate. Further¬
more, the strength of the silica sink (diatom productivity) is
at a maximum at intermediate river flows. This relation, which
is in agreement with other studies based on phytoplankton
abundance and enumeration, is significant to the extent that
diatoms are an important food source for herbivores.

The balance or lack of balance between nutrient sources and
sinks varies from one estuary to another just as it can from one
year to another within the same estuary. At one extreme, in
some estuaries river flow dominates the estuarine dissolved
inorganic nutrient distributions throughout most of the year.

At the other extreme, phytoplankton productivity dominates. In
northern San Francisco Bay, for example, the phytoplankton
nutrient sink is not as strong as in less turbid estuaries. In
this estuary, however, river effects, which produce or are as¬
sociated with near-conservative nutrient distributions, are
strong even at flows less than mean annual flow. Thus northern
San Francisco Bay appears to be an estuary between the two ex¬
tremes and is shifted closer to one extreme or the other, depend¬
ing on interannual variations in river flow.

Abstract from:

Cloern, J.E. and F.H. Nichols (eds.), 1985: Temporal Dynamics

of an Estuary: San Francisco Bay. D.W. Junk Publishers,

Dordrecht, the Netherlands.

33

THE IMPACT OF WATER DIVERSIONS
ON THE RIVER-DELTA-ESTUARY-SEA ECOSYSTEMS

OF SAN FRANCISCO BAY AND THE SEA OF AZOV

Michael A. Rozengurt, Michael J. Herz,
and Michael Josselyn

Paul F. Romberg Tiburon Center for Environmental Studies,
San Francisco State University

Abstract

A review of the long-term impact of river diversions on the
hydrological and biological features of the estuarine ecosystems
of San Francisco Bay and the Sea of Azov (once Russia's richest
fishing ground) indicates that despite differences in scale and
in climatic, hydrographic, and physiographic regimes, the eco¬
logical status of these systems, involving the River- Delta-
Estuary and adjacent coastal zone, depends on cumulative river
runoff fluctuations. In the past, before human intervention,
these systems were naturally maintained by stochastic processes,
but as a result of regulation of river flow during the last
30-40 years, these conditions have become primarily determinis¬
tic, artificially manipulated by man. Analysis of the relation¬
ships between water supply variables and parameters such as
salinity and catch of anadromous fish in both San Francisco Bay
and the Sea of Azov indicates that steady reduction of annual
and spring freshwater supply by diversions exceeding 30 percent
of the natural limits of the dominant fluctuations of these
estuarine ecosystems has resulted in drastic declines in the
fisheries.

Unprecedented changes in ecological conditions have
appeared 5-7 years after a period of 10-15 years of relatively
stabilized seasonal stream flows. These flows were at 30-65
percent of the mean historical water supply. The residual
inflow onto the estuary cannot entrain enough water to flush
wastes and excess salt into the sea and cannot provide the
optimal ranges of nutrients, salinity, and other dissolved
constituents necessary for the survival of estuarine species.

In the Sea of Azov, flow reductions have resulted in
increased salt intrusion from the Black Sea and have led to a
massive invasion of scvphozoan medusae, resulting in radical
declines in the economic and recreational significance of the
Sea since the late 1970s.

35

Introduction

Adaptation of estuarine organisms to a wide range of annual
and seasonal fluctuations in biochemical and biological charac¬
teristics is the result of centuries of evolution, in response
to the probabilistic nature of runoff variation. This process
has resulted in the ability to populations of estuarine orga¬
nisms to recover from extreme hydrological conditions, e.g.,
drought-produced, catastrophic declines in runoff leading to
salt intrusion, sporadic algal blooms, anoxia, etc. (Hedgpeth,

1970; L'vovich, 1974; Bronfman, 1977; Mann, 1982; and Rozengurt,
1974, 1983b). It is evident that the maintenance of estuarine
characteristics such as biological productivity and flushing
capacity are determined by the natural cycles of fluctuations of
freshwater supply to the system (Baydin, 1980). This inflow is
a renewable but limited resource.

Geophysical and climatological properties of the watershed
determine its volume and are important physical limitations that
should be considered an essential component of overall estuarine
resource management. Natural flow is a most essential factor to
be considered in analyzing any system (Champ et al. 1981;

Cronin, 1967; Lauff, 1967; Officer, 1976; and Vorovich et al.)
to determine what guantity of water can be diverted without
seriously damaging the estuary. However, the definition of
"natural flow" has been confused with a more limited concept of
"historic flow" based on the residual regulated flow, i.e., what
is left after upstream and within Delta diversions. From this
perspective "historic flow" is the unregulated runoff that
occurred during some past period, according to hydrological
definitions established by UNESCO (1974), and Sokolov and
Chapman (1974). Both recommend performing basin analyses on
unimpaired flow fluctuations over periods of at least 50-60
years.

To avoid confusion, it would be best to use the term
"historic" or "natural" when the figure concerned is the
unimpaired flow for all recorded years, and state the period
during which these baseline observations were made. Residual
flow should be considered as the net "regulated" rather than
"historic" flow.

Background

In estuaries which have a mean inflow significantly higher
than their total volume, the prevailing fluctuations of mean
freshwater supply (5 year running means of natural annual or
spring runoff under natural conditions) vary within 25 percent
of normal 50-60 year averages. Hence, if diversion within a
cycle, especially during periods of less than average flow, does
not exceed the natural deviations from the average flow, the
cumulative supply of the watershed may compensate for these

36

water withdrawals. In such a case, the estuarine ecosystem
would survive regulated water supply fluctuations because they
are within range of natural conditions. If diversions exceed
these natural limits for prolonged periods, there will be little
prospect of recovery because the natural resilience of the
system will be reduced and deteriorating conditions will produce
serious damage to its resources (Aleem, 1972; Rozengurt and
Haydock, 1981; and Rozengurt and Herz, 1981). In many parts of
the world, massive water diversions from estuaries have greatly
reduced or eliminated major fisheries, with annual losses
amounting to hundreds of millions of dollars, as a result of
destruction of habitats and degradation of conditions necessary
for reproduction and maturation (Aleem, 1972; White, 1977; Cross
and Williams, 1981).

In 1980, these problems were examined by the National
Symposium on Freshwater Inflow to Estuaries in San Antonio,
Texas. The Summary and Recommendations of this Symposium
included the following:

Published results regarding water development in rivers
entering the Azov, Caspian, Black and Mediterranean Seas in
Europe and Asia all point to the conclusion that no more
than 2 5-3 0 percent of the historical river flow can be
diverted without disasterous ecological consequences to the
receiving estuary. Comparable studies on six estuaries by
the Texas Water Resources Department showed that a 32 per¬
cent depletion of natural freshwater inflow to estuaries
was the average maximum percentage that could be permitted
if subsistence levels of nutrient transport, habitat main¬
tenance, and salinity control were to be maintained.

(Clark and Benson, 1981, page 524).

In the San Francisco Delta- Bay system where annual fresh¬
water flows have been reduced by as much as 62 percent (Nichols
et al. 1986), fish populations have declined radically. The
striped bass population is down to 2 0 percent and egg production
is at 10 percent of levels of the 1960s (Striped Bass Working
Group, 1982) and Chinook salmon population has declined to 30
percent of 1960 levels (Kjelson et al., 1982). Many other
investigators have attempted to quantify the relationship
between river flow and fish abundance with varying degrees of
success (Chadwick, 1971; Stevens, 1977; Smith and Kato, 1979).

Materials and Methods

In order to establish ecological criteria and make recommen¬
dations for management and protection of the San Francisco Bay
estuarine system, two crucial questions must be answered:

37

1. How much can be diverted from the watershed before
permanent damage is done to the ecosystem?

2. How much water must be released into the system in
order to mitigate the negative impact of water quality
after diversions have produced such damage, and is it
possible to maintain optimal levels of resources in the
estuarine system?

The Sea of Azov provides a comparative example of the
impact of water withdrawals on the physical and biological
characteristics of an estuary. In the large body of literature
produced in the Soviet Union since the 1920s, the Sea of Azov is
cited as the most productive low salinity region in the world.
According to Zenkevich (1963, p. 465) the total fish catch was
80 kg/hectare in some years. The case history of the Sea of
Azov is strong evidence in support of the concept that fresh¬
water inflow from its two main rivers, the Don and Kuban, plays
a major role in maintaining the biological productivity of the
Sea and its estuarine systems (GOIN, 1972; Bronfman, 1971;
Volovic, 1986).

The purpose of this research is to: (1) examine the
changes in the San Francisco Bay and the Sea of Azov ecosystems
(Table 1 and Figure 1) associated with freshwater diversion
patterns between 1921-1978; (2) analyze the relationship between
the modification of annual and seasonal river inflow, the water
quality of the ecosystem, and the status of its living and
non-living resources; and (3) attempt to define the levels of
river flow needed to meet the freshwater needs of these
resources while also satisfying the requirements of California's
agricultural, industrial, and municipal users.

The following data have been used in our analyses:

1. Monthly and annual natural and regulated river inflow
to the Delta, and the corresponding Delta outflow to
the Bay, for the period 1921-1978 (California
Department of Water Resources 1980; Kelley and Tippets,
1977).

2. Commercial and sport catches of anadromous fish
(striped bass [Mprqne saxatilis], and shad [Alosa
sapidissimal. from 1884 to 1982 (Skinner, 1962;

California Department of Fish and Game, 1983).

3. Monthly and annual values of combined natural and
regulated river inflow to the Sea of Azov, salinity of
sea water, and commercial catch records (1930-1980) of
major species of anadromous fish (publications of the
Ministry of Fisheries of the U.S.S.R., All Union Insti¬
tute of Fisheries and Oceanography, and the Azov- Black
Sea Institute of Fishery and other sources).

38

MORPHOMETRIC AND HYDROLOGICAL CHARACTERISTICS
OF THE RIVER-DELTA-ESTUARY-SEA ECOSYSTEM

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39

Figure 1 . Geographical maps of the Sea of Azov and its
basin watershed in the southern USSR and of the
San Francisco Bay/Delta watershed in the western United
States (common scale used for both maps) .

40

Results

The trend in fluctuations in natural runoff reflects
climatic cycles and their variations over large regions and is
not radically modified by man's activities (Figure 2). Analysis
of natural runoff cycles (11-15 years as described by L'vovich,
1979) in both the San Francisco Bay and Sea of Azov drainage
basins indicates the two are almost in phase, and therefore
suggests that any changes detected in regulated runoff are the
result of human modification rather than climatological factors.

An unusual feature of these variations is that the deviations of
mean runoff in each cycle vary within 25 percent of the average
perennial volume regardless of the magnitude of the annual mean
or seasonal discharges into either drainage basin.

Since the late 1950s, water withdrawals from the San
Francisco Bay watershed have increased from 20-30 percent of the
natural annual runoff to as much as 63 percent in 1977 (Figure
3 A) , and for the spring months of April, May, and June, they
have grown from 30-35 percent to 60-85 percent. For the Sea of
Azov, diversions have grown to as high as 46 percent (1974;

Figure 3B). This radical reduction of runoff superimposed on
natural cycles has diminished the water supply of the Delta and
Bay to levels below those observed for natural fluctuations for
annual or spring runoffs.

The deviations (for running averages of any 5-year period)
of regulated water supply to the Delta and Bay from "normal"
runoff have predominant ranges of -35 percent to -60 percent
(annual), and -40 percent to -85 percent for spring
(April-June) . Deviation for both natural, annual, and spring
5-year running means of Delta outflow, on the other hand,
generally vary around 15-25 percent of the mean (Figure 4 A-D).
This indicates that such extreme negative deviations did not
occur in the natural state of this estuarine system and have
only been seen since the onset of major human regulation.

Between 1955 and 1978, the period after the completion of
the Central Valley Project (CVP) and State Water Project (SWP),
major water storage and transport facilities, diversions
amounted to a total of 296 km3 of freshwater (240 MAF; Figure
5B) , equivalent to 40 times the volume of the San Francisco
Bay. Of this, 202 km3, or 164 million acre-feet (MAF), was
diverted from the rivers for irrigation and domestic water
supply and 94 km3 (76 MAF) was removed from Delta outflow for
agricultural and other needs. In other words, for 2 3 years, an
average of 8.8 km3 (7.1 MAF)/year was withdrawn from river
inflow to the Delta and 4.0 km3 (3.3 MAF) was removed from
Delta outflow to the Bay, yielding a total of 12.8 km3 (10.4
MAF) per year that never reached San Francisco Bay. For the
same period, (Figure 5 A) the total losses of freshwater supply
to the Sea of Azov accounted for almost 250 km3, or about 11
km3/year.

41

and (2) combined regulated river inflow to the Sea of Azov (dashed line
represents the average natural river inflow to the Sea of Azov, 1916-
1980).

44

— 1 - * - 1 - =-■ - 1 - . _ L- i 1 -l.i

1M° 1*40 1454 1*40 1*70 TMO

Year

Fig 2B. Fluctuations in the 5-year running average of (2) natural
inflow to the Sacramento-San Joaquin Delta and (3) regulated Delta
outflow to San Francisco Bay (dashed line represents the natural river
inflow to the Delta, 1 921-1978).

42

Y«ar

Fig. 3A. Fresh water diversions from the Sacramento-San Joaquin river
system expressed as the percentage of the annual natural river inflow to
San Francisco Bay.

Tl"1!!

1920

TT

1930

i n 1 1 1 i n 1 1 " 1 1 ■ ■ - n •

1940 v 1950 1960

TT

W70

Fig. 3B. Fresh water diversions from the Don-Kuban river system
expressed as the percentage of the annual natural river inflow to the Sea
of Azov.

43

40

Y • • r •

Fig. 4A. Annual percentage devia¬
tion of natural (1) and regulated
(2) Delta outflow from mean natural
Delta outflow (1921-1978 computed
with 5-year running means (annual
mean natural Delta outflow, 1921—
1978 = 27.7 million acre feet).

the month of May of natural (1) and
regulated (2) Delta outlfow from
mean natural Delta outlfow for May
(1921-1978), computed with 5-year
running means (May mean natural
Delta outflow, 1 921 -1 978 = 4.1 5

million acre feet).

*21 25 *31 35 *41 45 *61 55 *61 55 *7175

Y • a r •

Fig. 4B. Percentage deviation for
the month of April of natural (1 )
and regulated (2) Delta outflow for
April (1921-1978), computed with 5-
year running means (April mean
natural Delta outflow, 1921 -1 978 =
4.10 million acre feet).

Fig. 4D. Percentage deviation for
the month of June of natural (1)
and regulated (2) Delta outlfow
from mean natural Delta outflow for
June (1 921-1978), computed with 5-
year running means (June mean
natural Delta outflow, 1921 -1 978 =
2.51 million acre feet).

44

Salinity Increase* x 10b tonne* Lo**e»

300_

400

300

CO

2

200

100

0

300

250

200

u:

<

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o

K

150

100

50

Fig. 5 A . Cumulative curves: (1 ) freshwater

losses and (2) accumulation of salinity in the Sea
of Azov.

\

45

Volume ot Fresh Water

Fig. 5B. Cumulative quantity of freshwater
diverted (and so lost to the Delta/Bay system)
from withdrawals (l) within the Delta, (2)
upstream of the Delta and (3) combined.

46

K M

This pronounced trend of declining water supply had a
number of negative impacts on physical properties and biological
productivity of both the Sea of Azov and the San Francisco Bay
estuarine systems:

1. An increase in the frequency of salt intrusion into the
upper part of the Delta and Bay (Cloern and Nichols,
1985a; Nichols et. al. 1986) and, in the case of the

Sea of Azov, into the Don and Kuban River estuarine
systems (Bronfman, 1977; Remisova, 1984a, b) .

2. An increase of mean salinity in San Francisco Bay from
approximately 20 ppt (under outflow conditions of 34.2
kin3 or 27.7 MAF; Rozengurt, 1983b) to 27 ppt (15-17
km3 or 12.2-13.8 MAF) and, for the same period for
the Sea of Azov, from 9 ppt (43.0 km3) to 16 ppt
(21-25 km3). These changes represent mean increases
of 0.3 ppt and 0.4 ppt per hyrological year, respective¬
ly, for the two water bodies.

3. Significant reduction in the size and biological
productivity of the "entrapment" (null) zones have
occurred in the Delta and San Francisco Bay during the
summer months. Compression of these nursery zones,
their upstream movement, and the resulting changes in
their biochemical and biological properties have been
implicated as factors responsible for low survival
rates of eggs, larvae, and fry and for significant
population decreases (California Department of Fish and
Game, 1976; Herrgesell et. al. 1983; Cloern and
Nichols, 1985b).

4. Reduction of sediment load discharge to the Delta- Bay
Coastal Zone ecosystem (60-75 percent of the 8xl06
tonnes discharged per year for mean natural runoff
conditions; Krone, 1979). This leads us to speculate
that the absence of sediment may be partially responsi¬
ble for levee failures in the Delta as well as for in¬
creased beach erosion in the near coastal zone, since
both depend on deposition of sediment (each receives at
least 30 percent of the Delta and Bay's sediment load;
Kockelman et. al. 1982).

5. In the Sea of Azov, there has been a 60 percent
reduction in primary and secondary productivity and
over 95 percent reduction in catches of anadromous fish
(Goldman and Maysky, 1972; Makarov, et. al. 1982;
Remisova, 1984a, b: Figure 6A) resulting from
diversions of more than 60 percent of historic spring
(and more than 45 percent of annual) flows. Russian
scientists have determined that the reduction of runoff
of about 1 km3 reduces the Sea of Azov anadromous

47

fish stocks by about 3,000 tonnes (Marti and Musatov,
1973; Bronfman, 1977).

These flow modifications have also led to a 40-60
percent reduction in nutrient supply, decreases of
60-70 percent of sediment load and 80 percent reduction
in spawning and nursery areas, with salt intrusion
compressing the null zone into the pre- Delta and Delta
areas and salinity increasing from 0.5 to 10 ppt
(Baydin, 1980; Makarov, et al., 1982; Remisova,

1984a, b; Volovic, 1986). Numerous attempts to stop the
destruction of the Sea of Azov have failed. The
institution of extensive fishery regulations and the
release of more than 5.5 billion hatchery-reared fry in
1976 and hundreds of millions of fry of anadromous and
semi-anadromous fish between 1956-76 did not mitigate
the detrimental effect of excessive water diversions on
living resources of the ecosystem.

Further, when the mean salinity of the Azov seawater
stabilized at 14-16 ppt in the late 1970s (compared to
9.5 ppt in the 1930s), there was an invasion of marine
species. The billions of medusae (Figure 6B) that
moved into the Sea of Azov (Makarov, et al., 1982) and
into its formerly less brackish Taganrog Harbor and Don
River Delta (Figure 1) from the Black Sea presented a
serious threat to the survival of many indigenous
species. These jellyfish have created severe problems
in the Sea of Azov such as food competition between
them and fish, and public health problems along
hundreds of kilometers of beaches created by accumu¬
lation of dead medusae.

6. Although the San Francisco Bay estuarine system has not
yet deteriorated to the level of the Sea of Azov, the
impact of freshwater diversion on the survival of
living estuarine resources in both systems has many
alarming similarities: accumulation of organic and
inorganic compounds from agricultural drainage;
saltwater intrusion along the deep channels into the
Bay and Delta (Orlob, 1977); gradual salt buildup
throughout the estuary; and spontaneous algal blooms
(Cloern and Nichols, 1985a; Nichols et al., 1986). In
addition, the alteration of the Delta into a sophisti¬
cated plumbing system has led to disruption of fish
migration routes and their spawning and nursery areas
(Moyle, 1976; California Department of Fish and Game,
1976, 1983; Striped Bass Working Group, 1982;

Herrgesell, et al., 1983) and a significant reduction
of flushing intensity and circulation in all parts of
the Bay (Rozengurt, 1983a; Cloern and Nichols, 1985a).

All of these factors have contributed to diminishing

48

.,8000

'll . II . II . II . II . II . II

1920 1930 1940 1950 1960 1970 1980

Y*«r

Fig. 6A. Fluctuations in the 5 -year running average of ( 1 ) regulated
combined river inflow to the Sea of Azov and commercial catch of
anadromous fish (2) Russian sturgeon (Acipenser guldenstadti ) , Beluga
(Huso huso L.) and sevruga ( Acipenser stellatus Palas) , (3) Kerch ( Black
Sea) shad (Alosa kessleri pontica).

°a

CO

o

6.2

E

4c
j c
&

X

U)

12£

c

4

0

Fig. 6B -population explosion of the marine jellyfish (Aurelia) inside
the formerly brackish Sea of Azov as a result of increased freshwater
diversions and the resulting rise in salinity concentrations. (1) Annual
average salinity, (2) combined average annual freshwater diversions
expressed as a percentage of the natural runoff to the Sea of Azov, (5)
raw weight of jellyfish (Aurelia aurita and Rhizostoma) in millions of
tonnes, (6) combined number of jellyfish in billions.

49

Tonnes

catches of anadromous fish in the Bay and the adjacent
coastal zone, and threaten the sport landing of fish
and shellfish in the Bay as a whole.

7. Correlations of records of commercial catches of
salmon, striped bass, and shad with spring runoff to
the San Francisco Bay (2-4 year means) for pre-project
years (1915-1940) indicate that there were significant
landings only when spring Delta outflows were 3. 7-6. 2
km3 (3-5 MAF) for the preceeding 2-4 years. High
correlations between mean annual Delta outflow and
landings of striped bass, salmon, and shad strongly
support the hypothesis that at least 23.4 km3 (19.0
MAF) or 70 percent of the long-term average must reach
the Bay during the 3-5 years prior to the year of catch
to ensure successful commercial landings. The use of
lag times or averages of water flow over several years
to predict fishery abundance has been documented in
other estuarine systems (Therriault and Levasseur 1986;
Sutcliffe et al., 1977). It is important to use
averages which correspond to the reproductive maturity
of the fish. Figure 7 A-D shows some of these
correlations. In contrast, the current range of mean
annual and spring water supply to the Bay for the same
time lag is 1.5-2. 5 and 2-5 times less than the long¬
term average, respectively. The relative value of
negative deviations of 5-year running mean freshwater
supply to the Bay has dropped 60-85 percent below
"normal" spring, and 45-60 percent below "normal"
annual Delta outflow for the period 1921-1980.

In recent years, commercial fishing has been prohibited
in San Francisco Bay and Delta waters (since the late
1950s for salmon and shad, and since 1935 for striped
bass). Nevertheless, sport catches of these species
have declined to as little as 3 0 percent of levels of
20 years ago despite a great increase in sportfishing
effort, improved treatment of sewage discharges, and
massive hatchery releases.

8. Figure 8A illustrates the steady decline of 3-year
running means of regulated spring Delta outflow since
1954. The deviations (negative) of water supply to the
Bay from mean natural Delta outflow were nearly 80
percent for most of the springs of the 1970s (Figure
8B) . This demonstrates that the estuarine system was
deprived of significant amounts of freshwater and
implies that the high levels of diversion are responsi¬
ble for the drastic decline in striped bass catches
(Figure 8C) and the Striped Bass Index (Figure 8D).

Note the relationship between flow (Figure 8A), and
catch (Figure 8C) with 3-year lag, e.g., 1954-56

50

■1 7.29 + 6.47 lnX
0. 80

•w»

•mo

• 1017

• 101*

• mi
• mi

• 1022

'•a ^

• • 1020

3000

2000

10 20 % 30 40

l 10 A.F.

Fig. 7A. The relationship between annual salmon catch in the Sacramento -
San Joaquin rivers and upper San Francisco Bay and the mean regulated
Delta outflow to San Francisco Bay for five running years. Each salmon
catch is the amount caught in the last year of five previous running
years of outflow (e.g. salmon catch for 1918 is based on outflow for
1914-1 91 9) .

3000

2000

1000

0

- 1 _ , _ I _ . _ l _

2.0 4.0 6.0

KM

Fig. 7B. Ibe relationship between annual commercial salmon catch in the
Sacramento-San Joaquin rivers and upper San Francisco Bay and the mean
Delta regulated outflow for a period of three running months (April -May-
June). Each year's salmon catch is based on a lag outflow period of two
years after the last spring Delta outflow to the Bay and for two years
previous (e.g. salmon catch for 1916 is based on Apri 1-May-June outflow
for 1912-1 91 4).

51

- - - 1 . _ 1 . . i- - -

20 , M 40

KM

Fig. 7C. The relationship between annual shad catch in the San Francisco
Bay area and the mean regulated Delta outlflow to San Francisco Bay for
two running years. Each annual catch is based on a lag outflow period of
one year after the last of two years of previous Delta outflow (e.g. shad
catch for 1916 is based on outlfow for 1914-1915).

2-0 40 6 0

KM

Fig. 7D. The relationship between annual striped bass catch in the San
Francisco area and the mean Delta regulated outflow to San Francisco Bay
for a period of three running months ( April-May -June) . Each annual
striped bass catch is based on a lag outflow period of two years after
the last spring Delta outflow bo the Bay and for two years previous (e.g.
striped bass catch for 1917 is based on Apr il -May -June outflow for 1913-
1915) .

52

Ton*

3.59 x *)6 A.F. (1921 -1978)

q.40

jl!

ill

1960 1965 1970 1975

Ytiri

1980

1985

Fig. g. (A) Fluctuations of Delta regulated water supply to San
Francisco Bay during spring (April-June). Data represent 3-year running
means (e.g., 1958-1 960). (B) Deviation in percentage of Delta regulated

water supply to San Francisco Bay of mean spring natural runoff. (C-1)
San Francisco Bay striped bass party boat catch/angler day (1 959-1 982).
( C — 2 ) Total striped bass party boat catch/season in number of fish
(1 959-1982). (D-1 ) Annual juvenile striped bass abundance index (1959-

1985). ( D-2) Five-year running means of striped bass abundance index

(1 959/63-1 981/85).

53

flow/1959 catch). Regressions between sportfishing
catches of striped bass for this period and Delta
outflow for the 3 years preceeding the year of catch
with a 0-2 year time lag are similar to those between
striped bass commercial catch and flow shown in Figure
8.

9. In the literature on the status of Chinook salmon
spawning populations in the Sacramento-San Joaquin
watershed, four factors have been proposed to explain
their precipitous population decline: dams, water
diversions, pollutants, and the loss of habitat
(California Department of Fish and Game, 1983). The
early winter run is considered a major source of
recruitment for this stock (Hallock and Fisher, 1985).
Between 1967-1982, when reliable counts were made of
winter salmon runs, the 5-year running means of regu¬
lated spring water supply to the estuary was about
35-80 percent of spring perennial mean runoff (1921-
1978). The average annual volume of water diversion
was approximately 12.2 km3 (11.0 MAF; Figure 9) and
cumulative withdrawals from the Sacramento-San Joaquin
river water supply to the estuarine system reached
about 190 km3 (158 MAF; Figure 9A) between 1967 and
1982. During the same period the number of winter-run
Chinnok salmon returning to spawn in the upper part of
the Sacramento River was reduced as much as 60 times
(Figure 9D, Hallock and Fisher, 1985) despite attempts
to mitigate this decline with release of millions of
hatchery-reared juveniles (Figure 9C, California
Department of Fish and Game, 1983).

While all of the factors mentioned above may contribute to
reduction of the salmon population in this watershed, our data
strongly suggest that overall reduction of runoff and cumulative
losses of water and biochemical constituents resulting from
diversions will continue to be the principal factors governing
migration, spawning success, and recruitment in this stock.
Kjelson et al. (1982) also attribute decreases in salmon
populations to increases in water diversions. They found that
the March-June runoff of up to a total of 8.6 km3 (7 MAF),
lagged 2.5 years, may provide optimal conditions for Chinook
salmon spawners during nursery migration. Similar deterioration
of ecological conditions and biological productivity following
excessive freshwater withdrawals has occurred in estuaries in
Africa, Asia, Australia, Europe, and the United States.

(Hedgpeth, 1970; Aleem, 1972; Baydin, 1980; Cross and Williams,
1981; L'vovich, 1974; Meleshkin et al., 1973; Mancy, 1979;
Rozengurt, 1971, 1974, 1983a, b; Rozengurt and Herz, 1981; Mann,
1982; Tolmazin, 1985; and White, 1977).

54

A

Fig. 9. (A) Cumulative combined upstream diversions of the Sacramento-

San Joaquin river systems (1 967/69-1977/78). First data point is sum of
diversions from 1955-1967. (B) Annual gross upstream diversions of the

Sacramento -San Joaquin river systems (1967-1978). (C) Annual release of

yearling chinook salmon juveniles from California State hatcheries (1970-
1981). (D) Five-year running mean of winter-run spawning salmon past

the Red Bluff diversion dam (1967/71 -1 980/84).

55

Conclusions

Since the late 1950s, diversions of water from the San
Francisco Bay watershed have increased from 20-30 percent to as
much as 63 percent annual runoff and from 30-35 percent to 60-85
percent for spring runoff (April-June) . During the same period,
the predominant ranges of negative deviations from the "normal"
runoff (1921-1978) for the 5-year running means of annual dis¬
charges (regulated) to the Delta and Bay is 35-60 percent, the
range is 40-85 percent for the spring discharges. Without regu¬
lation, outflow deviations of natural water supply for both
annual and spring 5-year running means of normal runoff varied
only 15-25 percent from the same mean value. Overall, between
1955 and 1978, (a period when the major water storage and
diversion facilities were fully operational about 286 km3 (240
MAF), or as much as 40 times the volume of San Francisco Bay,
was diverted from the system.

These reductions of freshwater flow to the estuary have:
greatly increased salt intrusion into Delta waters, threatening
agricultural and municipal water intakes; produced massive
reduction of nutrients and sediment load; and greatly reduced
flushing and circulation activity formerly accomplished by heavy
spring inflows.

Concurrent with these flow-related changes, there have been
massive reductions of fish populations. Salmon are down to 30
percent of 1960s levels, while striped bass are down to 2 0
percent of their levels of 20 years ago. Statistical analyses
reflect an underlying relationship between catch of salmon,
striped bass, and shad and freshwater flow to the estuary for
the preceeding 2-4 years.

High correlations obtained between commercial fish catches
(prior to construction of California water projects) and running
mean Delta outflow indicate that annual water supply had to be
at least 23.0 km3 (19.0 MAF) and spring runoff (April-June) in
the range of 3. 1-3. 7 km3 (2.5-3. 0 MAF), 69 percent and 68-84
percent of the historic unimpaired flow, respectively, for the
2-4 preceding years to ensure optimal commercial catch. Similar
analyses for successful sportfishing catches (post project
construction) show that annual mean flows of 21.0 km3 (17.0
MAF) and spring Delta outflows of 2. 5-3.1 km3 (2. 0-2. 5 MAF)
are needed for the 2-3 preceding years to ensure significant
catches. However, during 1967-1982 (CVP and SWP operating at
full capacity), the 3-5 year running mean spring and annual
water supply into and out of the Delta was several times less
than this.

The result has been a major impact on recruitment and
recreational catches of striped bass and salmon since the late
1960s. Salmon and striped bass natural reproduction has been
reduced 65 percent and 80 percent, respectively, over the past

56

20 years (California Department of Fish and Game 1983). The
direct economic impact for the last two decades has been losses
of about 1.3 billion dollars (Meyer Resources, 1985).

In the Sea of Azov, diversions of more than 60 percent of
historic spring (and more than 45 percent of annual) flows have
resulted in:

1. Distortion of circulation dynamics and reduction in
vertical mixing (increases in vertical stability index)
as much as 3-5 times resulting in significant increases
in frequency of anoxic conditions in deep water near
the bottom, covering as much as 60 percent of the sea
area (Volovic, 1986).

2. Accumulation of more than 1,500 x 106 tonnes of salt
and an overall increase of the mean salinity from 9-9.5
to 14-16.0 ppt and in the pre-Delta areas from 0. 5-3.0
to 6-10.0 ppt for the last two decades.

3. Reduction of 60-75 percent (2 x 106 tonnes) in sedi¬
ment load, and 80 percent in spawning and nursery
areas.

The resulting economic losses for fisheries since the late 1960s
have been tens of millions of dollars per year (Meleshkin et.
al. 1973, 1981; Vorovich et. al. 1981).

These and other similar historical examples of the relation
between human needs for freshwater and protection of estuarine
environments (Mann, 1982; Meleshkin, 1981; Rozengurt and
Tolmazin, 1974; Rozengurt and Herz, 1981) indicate that special
consideration should be given to the consequences of timing and
volume of water withdrawals on recruitment and landings of
anadromous fish, because of their sensitivity to cumulative
fluctuations in freshwater supply. It may be possible to
alleviate these problems and to protect freshwater intakes in
the Delta if limits to water diversion can be agreed upon.
Perhaps this can be done through the establishment of salinity
and flow standards for San Francisco Bay (neither of which
currently exists). In addition, Rozengurt (1983a) has suggested
a restraining channel be constructed in part of the existing
ship channel in San Pablo Strait (2 walls 1-3 kilometers long
and 200 meters apart, extending from the bottom to just above
the high tide level). Hydrological model testing of this design
will be required to determine its effectiveness in limiting salt
intrusion into Suisun Bay and the Delta (Rozengurt, 1971, 1974).

57

Acknowledgements

This research was supported by grants from the San
Francisco Foundation/Buck Trust. The authors gratefully
acknowledge the critical comments and editorial and cartographic
assistance of Professor Joel W. Hedgpeth and technical help by
Douglas Spicher.

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Wldlife Resources of the San Francisco Bay Area. Sacra¬
mento, CA. Department of Fish and Game, Water Projects
Branch, Report #1.

Smith, S.E., and S. Kato, 1979: The fisheries of San Francisco
Bay: Past, present, and future. In Conomos, T. (Ed.) San

Francisco Bav: The Urbanized Estuary. San Francisco.
Pacific Division of the AAAS 445-468pp.

Sokolov, A. A., and T.G. Chapman (eds.) 1974: Methods for Water
Balance Computations. Paris. UNESCO Press.

Stevens, D.E., 1977: Striped Bass (Morone saxatilis) year class
strength in relation to river flow in the Sacramento-San
Joaquin estuary, California. Transactions of the American
Fisheries Society. 106:34-42.

Striped Bass Working Group, 1982: The Striped Bass Decline in
the San Francisco Bav-Delta Estuary. Sacramento, CA.
California State Water Resources Control Board.

Tolmazin, D.M., 1985: Changing coastal oceanography of the

Black Sea. In: M.U. Angel and R. Smith (eds.) Progress
in Oceanography Volume 15. New York, Pergamon Press,

2 17-276pp.

UNESCO, 1974: International Glossary of Hydrology. Geneva,
UNESCO Press, p. 90.

Volovic, S.P., 1986: The fundamental features of transformation
of the Sea of Azov ecosystems in connection with industrial
and agricultural development in its watershed. Voprocv
Ikhtiology (The Problems of Ichthyology). Ac. of Sci.,

USST, V. 6. 1:33-47. (In Russian; English translation,
Scripta Technica, Wiley & Sons, 1986).

Vorovich, I. A., Gorstko, A.B., and Dombrovsky, U.A., 1981:

Rational use of the Sea of Azov resources: mathematical
modeling. Nauka ("Science"), Moscow, 359pp.

White, G. (ed.) 1977: Environmental Effects of Complex River
Development. Boulder, CO. Westview Press.

Zenkevitch, L. 1963: Biology of the Seas of the U.S.S.R.

London, George Allen and Unwin, Ltd.

62

THERMAL DYNAMICS OF ESTUARINE PHYTOPLANKTON:

A CASE STUDY OF SAN FRANCISCO BAY

James E. Cloern, Brian E. Cole, Raymond L.J. Wong
and Andrea E. Alpine
U.S . Geological Survey

Abstract

Detailed surveys throughout San Francisco Bay over an annual
cycle (1980) show that seasonal variations of phytoplankton
biomass, community composition, and productivity can differ
markedly among estuarine habitat types. For example, in the
river-dominated northern reach (Suisun Bay), phytoplankton
seasonality is characterized by a prolonged summer bloom of
netplanktonic diatoms that results from the accumulation of
suspended particulates at the convergence of nontidal currents
(i.e. where residence time is long). Here turbidity is persis¬
tently high, such that phytoplankton growth and productivity are
severely limited by light availability, the phytoplankton popula¬
tion turns over slowly, and biological processes appear to be
less important mechanisms of temporal change than physical pro¬
cesses associated with freshwater inflow and turbulent mixing.
South Bay, in contrast, is a lagoon-type estuary less directly
coupled to the influence of river discharge. Residence time is
long (months) in this estuary, turbidity is lower and estimated
rates of population growth is high (up to 1-2 doublings d”1)
but the rapid production of phytoplankton biomass is presumably
balanced by grazing losses to benthic herbivores. Exceptions
occur for brief intervals (days to weeks) during spring when the
water column stratifies so that algae retained in the surface
layer are uncoupled from benthic grazing, and phytoplankton
blooms develop. The degree of stratification varies over the
neap-spring tidal cycle, so South Bay represents an estuary
where: (1) biological processes (growth, grazing) and a

physical process (vertical mixing) interact to cause temporal
variability of phytoplankton biomass; and (2) temporal vari¬
ability is highly dynamic because of the short-term variability
of tides. Other mechanisms of temporal variability in estuarine
phytoplankton include zooplankton grazing, exchanges of micro¬
algae between the sediment and water column, and horizontal
dispersion, which transports phytoplankton from regions of high
productivity (shallows) to regions of low productivity (deep
channels) .

Multi-year records of phytoplankton biomass show that large
deviations from the typical annual cycles observed in 1980 can
occur, and that interannual variability is driven by variability
of annual precipitation and river discharge. Here, too, the
nature of this variability differs among estuary types. Blooms
occur only in the northern reach when river discharge falls

63

within a narrow range. The summer biomass increase is absent
during years of extreme drought (1977) or years of exceptionally
high discharge (1982). In South Bay, however, there is a direct
relationship between phytoplankton biomass and river discharge.
As discharge increases so does the buoyancy input required for
density stratification, and wet years are characterized by
persisent and intense spring blooms.

REFERENCES

Cloern, J.E. and F.H. Nichols (eds.), 1985. Temporal Dynamics of
an Estuary: San Francisco. D.W. Junk Publishers, Dordrecht,
The Netherlands.

64

BENTHIC ECOLOGY AND HEAVY METAL ACCUMULATION

Frederick H. Nichols
U.S . Geological Survey

Abstract

The benthos of San Francisco Bay (the comrftunity of inverte¬
brates living in bottom sediments) is an important source of
food for fish, birds, and humans, and is dominated by exotic
species introduced during the past 130 years. These species are
largely small, hardy, short-lived, rapidly-reproducing species
(much like weeds) whose distributions and abundances vary widely
in both space and time. As a result, they appear resilient in
the face of both natural and human-induced disturbances.

The Bay's benthic organisms are contaminated to varying
degrees and, in some cases, physiologically affected by wastes.
Contaminant concentrations vary seasonally, annually, and with
proximity to contaminant sources. There is an apparent but not
clearly understood relationship between river flow and the
accumulation of wastes in the estuary's sediments and organisms.
However, effects at the community level are not easily distin¬
guished from natural variability.

Variations in river flow can have a marked effect on the
distributions and abundance of benthic animals, thereby affect¬
ing local food web dynamics. During periods of persistently low
flow, for example, benthic invertebrates can become relatively
more important in the northern part of San Francisco Bay and, as
a result, compete with the small pelagic animals (that are food
for fish) for the phytoplankton produced there. The benthos is
apparently important in preventing eutrophication in San
Francisco Bay by consuming phytoplankton before it can grow to
nuisance levels.

Introduction

The "benthos" is the community of invertebrate animals
(worms, clams, shrimps, etc.) living on the bottom of aquatic
environments. These animals consume organic matter that grows
on or settles to the bottom and, in turn, become food for fish
and other consumers, including humans. They are often sessile,
living most of their life in the same location. Thus, they
provide a continuing record, through changes in species composi¬
tion or abundance or the effects of both short- and long-term
changes in the environment. This feature had lead to their use
as indicators of water pollution.

Introduced Species

Today, the benthos of San Francisco Bay is composed largely
of introduced exotic species, many having arrived with the

65

oysters that were shipped from the U.S. East Coast for growing
in the Bay. Others arrived in ballast water or burrowed into
the wood hulls of ships arriving from ports all over the world
(Carlton, 1979). These are hardy, opportunistic species, much
like weed plants, that are seemingly resilient to disturbance.

They may be temporarily eliminated from a given location in the
Bay as a result of some natural (e.g., a storm or a prolonged
wet or dry period) or human-induced (dredging) disturbance. How¬
ever, these animals typically return soon after the disturbance
has ceased. It is against this background of high variability
and apparent resilience that we must assess human effects.

Effects of Waste Discharge

The effects of waste discharge into the Bay were noted as
early as 1900, when oyster beds were observed to be contaminated
with human and industrial sewage. Soon thereafter, the taste of
the harvested oysters began to deteriorate, and growth was im¬
paired. By the 1930s, the oyster industry had failed. Through
the 1950s, raw or poorly treated sewage killed bottom organisms
through lack of oxygen, and shellfish were contaminated with hu¬
man enteric bacteria. Beginning in the 1960s, the construction
of facilities to treat waste began to resolve the oxygen and
coliform bacteria problems, and by the 197 0s, these problems had
been largely resolved (Nichols et. al. 1986).

Now, industrial chemicals (some of which are known to be
toxic) have become the primary concern. The tissues of mussels
and clams contain varying levels of industrial chemicals depend¬
ing on their proximity to sources of contaminants, time of year
and, apparently, the relative rate of freshwater inflow. For
example, concentrations of the trace metal silver (a contaminant
whose sources are largely the photographic and electronics in¬
dustries) in South Bay clams vary seasonally and between years
(Luoma et. al. 1985). Highest seasonal levels are found fol¬
lowing the initial storms and runoff of winter while highest
annual levels are found during driest years, These results
suggest that river flow is important in the assimilation and/or
flushing of contaminants from the Bay. However, the mechanisms
are not well understood. Experimental studies have shown that,
through genetic flexibility, some individuals within a species
can survive in environments with high contaminant levels while
other cannot (Luoma et. al. 1983). These studies have demon¬
strated that clams are physiologically stressed during periods
when contaminant levels in the environment are highest.

Despite clear evidence that individuals of many species
contain contaminants, we have difficulty demonstrating a re¬
lationship between contaminated individuals and a threatened
population. That is, we have not clearly demonstrated that
there have been significant declines in either the abundance of
the species Bay-wide or in the importance of these species in
the Bay's food webs because of contamination with toxic
chemicals. This difficulty results from: (1) the extreme

66

variability in the seasonally and interannual patterns of abun¬
dance that are most easily ascribed to natural causes; (2) the
apparently hardy nature of many of the species; and (3) the lack
of appropriate studies to prove or disprove cause and effect
(Nichols et. al.. 1986).

Effects of the Benthos on the Pelagic Food Web

Because the estuary is shallow and the water in it well
mixed, phytoplankton (microscopic single-celled plants growing
in the water column that form the base of aquatic food webs) are
directly available to benthic animals that filter food particles
out of the water. Because of their great abundance, benthic fil¬
ter feeders may act as a natural biological control on eutrophi¬
cation -- the growth of nuisance phytoplankton blooms in aquatic
systems in response to enrichment with nutrients such as nitro¬
gen and phosphorus (Cloern, 1982). Eutrophication in estuaries
often leads to the depletion of oxygen in the water and the sub¬
sequent death of aquatic animals. By removing phytoplankton as
fast as they grow, benthic invertebrates in San Francisco Bay
convert sewage-derived nutrients directly into animal biomass.
Thus, the Bay is not subject to noxious accumulations of excess
phytoplankton (Nichols et. al. 1986). We can conclude from this
finding that processes that could selectively disturb the ben¬
thos, such as severe contamination with pollutants, might permit
the development of nuisance blooms and anoxia in San Francisco
Bay. Occasionally, localized, thick mats of decaying macroalgae
become deposited on intertidal mudflats and smother resident
benthic animals (Nichols and Thompson, 1985). These occurrences
are unpredictable and only partially understood.

Whether the direct removal of phytoplankton by benthic
filter feeders actually inhibit overall productivity of the
estuary is not clear. However, during the 1976-77 drought, the
high salinity of northern San Francisco Bay during two
successive winters permitted the establishment of large
populations of benthic animals that, in turn, may have been
responsible for the unusual declines in phytoplankton,
zooplankton, shrimp, and larval striped bass (Nichols, 1985).

The implication from these observations is that during any
future periods of persistently low flows when winter salinity
levels remain high, the food web in northern San Francisco Bay
may shift from pelagic type, culminating in the striped bass, to
a benthic type, culminating perhaps, in less important demersal
fish species.

67

REFERENCES

Carlton, J.T. 1979: Introduced invertebrates of San Francisco
Bay. in T.J. Conomos, (ed.), San Francisco Bay, the
Urbanized Estuary. Pacific Division, Amer. Assoc. Adv. Sci.,
San Francisco, Calif, 427-444.

Cloern, J.E. 1982: Does the benthos control phytoplankton

biomass in south San Francisco Bay? Mar. Ecol. Prog. Ser.
9:191-202.

Josselyn, M.N. and J.A. West, 1985: The disturbance and

temporal dynamics of the estuarine macralgal community of
San Francisco Bay. Hvdrobioloqia 129: 139-152.

Luoma, S.N., D.J. Cain, K. Ho, and A. Hutchinson, 1983:

Variable tolerance to copper in two species from San
Francisco Bay. Mar. Environ. Res. 10: 209-222.

Luoma, S.N., D.J. Cain, K. Ho, and C. Johansson, 1985: Temporal
fluctuations of silver, copper, and zinc in the bivalve
Macoma balthica in five stations in South San Francisco
Bay. Hvdrobioloqia 129: 109-120.

Nichols, F.H., 1985: Increased benthic grazing: an alternative
explanation for low phytoplankton biomass in northern San
Francisco Bay during the 1976-77 drought. Estuar. Coast.
Shelf Sci. 21:379-388.

Nichols, F.H., J.E. Cloern, S.N. Luoma, and D.H. Peterson, 1986:
The modification of an estuary. Science 231:567-573.

Nichols, F.H. and J.K. Thompson, 1985: Time scales of change in
the San Francisco Bay benthos. Hvdrobioloqia 129:121-138.

68

AGENCY COOPERATION AND FISHERY STUDIES

IN SAN FRANCISCO BAY

Perry L. Herrgesell

California Department of Fish and Game

Abstract

The people of California have been divided on many environ¬
mental issues, but governmental cooperation and coordination at
both state and Federal levels is beginning to mitigate the im¬
pacts of this division. Four agencies (California Department of
Water Resources, California Department of Fish and Game, U.S.
Bureau of Reclamation, and U.S. Fish and Wildlife Service) have
signed a Memorandum of Agreement that established the Inter¬
agency Ecological Study Program. This program has provided for
the performance of studies necessary to obtain a thorough under¬
standing of the requirements of the fish and wildlife resources
in the estuary and how these requirements relate to water pro¬
jects. This has helped bridge the gap between environmentalists
and water developers. One of these interagency studies is
documenting the importance of freshwater flows and water project
activities to the Bay system downstream of the Delta. The Delta
Outflow/San Francisco Bay Study has shown that fish and shrimp
abundance and distributions appear to be related to freshwater
inflows from the Delta. If divisive environmental issues are to
be adequately resolved in California, continued studies as well
as continued financial and political support are needed. Early
results from the biological portion of the Delta Outflow Study
must be quantified and related to results from the recently
implemented hydrodynamic elements. Finally, a long standing
controversy regarding the Federal Central Valley Project's role
in protecting beneficial uses in the system has been resolved to
the state's satisfaction in the Coordinated Operations Agreement
(COA).

The Bible describes how a group of people were led from
Egypt and came to the waters of the Red Sea. The account re¬
lates that their leader raised his staff and divided the waters
so that the people could pass through and escape destruction
from their enemies. In California, this age-old story has been
reversed. If one reviews the history of the state's water pol¬
icy development, he will find that water, through its unequal
distribution in the state, has divided the people. Most of the
population and, therefore, the political power resides in the
relatively dry, southern part of the state, while most of the
rainfall occurs in the northern part of the state and flows
through the San Francisco Bay estuary to the Pacific Ocean.

69

Because of this fact divisions have developed between citizens
of the north and south, between farmers, and the urban dwellers,
between developers and environmentalists, and between politi¬
cians and the lay public. These groups became more polarized,
when the Bureau of Reclamation in about 1951, and the State
Department of Water Resources in about 1968, began diverting
water from rivers in the northern part of the state, such as the
Sacramento and the San Joaguin, for use in the south.

One can make three basic points about California water and
its management as it relates to fish and wildlife resources in
California: (1) California is divided in many ways on many

environmental issues, but government cooperation and coordina¬
tion, at both the state and Federal levels is beginning to
mitigate the impact of this division; (2) multi-agency, scienti¬
fic fish and wildlife studies are documenting the importance of
freshwater flows and water project activities on the Bay system;
and (3) continued studies are needed, in addition to continued
financial and political support, if divisive environmental
issues are to be adequately resolved.

Government Cooperation and Coordination

In 1970, when it became common knowledge that fish and
wildlife problems existed in the estuarine system, and that one
of the factors responsible for those problems was the Federal
Central Valley Project and the State Water Project, four state
and Federal agencies executed an Interagency Memorandum of
Agreement. These agencies were: the Department of Water
Resources (DWR) , California Department of Fish and Game (DF & G),
the U.S . Bureau of Reclamation (USBR), and the U.S. Fish and
Wildlife Service (USFWS). The purpose of this agreement was to
provide for the performance of studies that would be necessary
to obtain a thorough understanding of the requirements of the
fish and wildlife resources in the estuary. These studies also
represented significant follow-up efforts to cooperative work
that began early in the 1960s between the DWR and DF & G.

All the agencies in this group agreed that it was necessary
to define design and operation criteria for the projects, in
order that resource protection could be assured. This coopera¬
tive alliance between water development agencies and fish and
wildlife agencies was the first major fish and wildlife accom¬
plishment associated with water policy in California.

The intent of this so-called "Interagency Ecological Study
Program" was good, but true to California's divisive nature, the
estuary was divided into two components, and only the upstream
Delta portion of that system was studied in detail. Cooperative
work was carried out during the early 1960s and 1970s and
yielded much information about fishery resources and their

70

relationship to water diversion projects. Specifically, these
studies and cooperative efforts learned six important things:

(1) striped bass and pelagic fish eggs were being diverted from
the system; (2) the louver fish screen efficiencies at the
intake of state and Federal water diversions, depending on the
species and life stages, were quite low, ranging from about 5 to
80 percent, (3) water diversions act as density independent
sources of mortality for young striped bass; (4) flow reversals
which were associated with pumping confuse young adult fish
migration; (5) pumping increases flow velocities in channels,
and that in turn reduces the standing crop of food organisms
that are produced there; and (6) the actual magnitude of flow
passing through the Delta into the Bay affects the distribution
and abundance of fish and their food organisms.

This information was used for two significant purposes in
California. First of all, it was used to develop recommenda¬
tions for the controversial Peripheral Canal. This was a
structure proposed for diverting water around the Delta system
for transport to the southern part of the state. Secondly, the
information developed by the Interagency Program was used in
1978 by the regulatory State Water Resources Control Board to
develop standards to protect beneficial uses in the Delta
component of the system. The Board adopted Water Rights
Decision 1485, which innovatively established flow/salinity
standards necessary to protect fishery resources in the estuary
based on information available at that time. However, there was
still division. The studies were looking at the Delta and not
the Bay portion of the estuary. In adopting D-1485, the State
Board took another positive step to bridge this division. They
mandated, in D-1485, that flow studies would be carried out in
the Bay, downstream of the Delta, and that these studies would
be paid for by the water diversion permit holders; in this case,
the Department of Water Resources and the Federal Bureau of
Reclamation. The Interagency Program already in place became
the vehicle to implement this study in 1980.

Biological portions of the Delta Outflow/San Francisco Bay
Study began in 1980, but again division occurred. This time,
the division was regarding the roles of hydrodynamic and fishery
studies. While the fishery studies continued, project
biologists and engineers debated the following questions: "What
should be the driving force for the Bay outflow study?" In
other words, should biology precede hydrodynamic work and
provide the basis for the structure of hydrodynamic study plans
or should hydrodynamics precede biology? This issue remained
unresolved for about four years until it was agreed that the
hydrodynamic program should answer "biologically relevant
hydrodynamic questions." In other words, the study would be
based on the needs of the biological program.

The hydrodynamic study plan which was implemented earlier by
DWR was augmented in 1984 and interagency cooperation again
bridged another division. At this time, two more agencies

71

joined the Interagency Program. Those agencies were the U.S.
Geological Survey (USGS) and the State Water Resources Control
Board (SWRCB). Today, a six agency program exists instead of a
four agency program.

The overall goal of the Delta Outflow/San Francisco Bay
Study is to determine the relationship between freshwater
outflows and fish and wildlife resources in the Bay, downstream
of the Delta. In order to attain this goal, four general ob¬
jectives are being pursued. First of all, the study is deter¬
mining what elements of the Bay biota would be affected by signi¬
ficant changes of the inflow of freshwater from the Delta.
Secondly, the project is determining how the flow reductions
associated with the state and Federal project operations would
change hydraulics and salinity gradients in the Bay. Thirdly,
the effect of changes in hydraulics and salinity on the fish and
wildlife resources in the Bay will be investigated. Finally,
all this information will be used to develop flow and salinity
standards (or other management strategies) if necessary to
better protect fish and wildlife resources of the Bay.

These objectives are being met through a twofold approach.
First of all, fishery studies are being carried out in the Bay
itself. By collecting monthly fishery samples at 3 5 locations
in the Bay, the distributions and abundances of fish, shrimp,
and crabs are being documented. This data will then be combined
with output from the second aspect of the program -- the Hydro¬
dynamic/Physical/Chemical study. This recently expanded study
element is evaluating changes in salinity and circulation
patterns that are caused by outflow variation. These evalua¬
tions are being done using modeling work carried out by a
five-member modeling team that is working under the technical
supervision of Dr. Ralph Cheng, of the U.S. Geological Survey in
Menlo Park, California.

Parenthetically, the Interagency Program represents
substantial funding commitments by the agencies involved. For
example, the fiscal year 1985 budget for the Interagency Program
is about $4,906,000. That money is allocated between five major
programs including the San Francisco Bay/Delta Outflow Study.

This study alone represents a budget of $1,655,000 for the
coming year.

Study Results

To date, the fishery data collected in the outflow program
have only been summarized for the first three years, but it is
interesting because considerable variation in outflow has
occurred during this year. The year 1981 was dry, while 1980
and 1982 were wet years. Of the wet years, 1982 provided the
highest amount of outflow to the bay. Additionally, the
hydrographs for these years are characterized by pulse periods,
when flows were considerably greater than other periods. These
pulses are short-term high flows that move through the system,
greatly altering physical conditions.

72

To date, about 109 species of fish have been collected from
the Bay. These species have been distributed among 43 different
families. More importantly, it appears that fish abundance and
distributions are related to freshwater inflow from the Delta.

For example, of the 58 species looked at so far, 24 demonstrated
a "wet response" to flow. In other words, these species were
caught in greater numbers during wet years. Twenty-two species
showed a mixed response, while only 12 showed a dry response
(Table 1).

Table 1. Number of species with highest catches during
various year types.

Salinity Preference Wet

_ Group _ Response

Freshwater 3

Anadromous 3

Estuarine 5

Marine-Estuarine 2

TOTAL 24

Mixed

Response

3

3
2

4

22

Dry

Response

2

1

0

2

12

A surprising thing was learned upon further analysis of
these same data when individual species responses were cate¬
gorized (Table 2). Only one species in the top 15 most abundant
species demonstrated a dry response. That species was the
jacksmelt. This is interesting because one would expect greater
numbers of marine species in the Bay during dry years. This did
not occur. It is also interesting to note the estuarine species
response (Table 2). Four of the five estuarine species col¬
lected occurred in the top 15 of the most abundant species in
the Bay, and all of those species demonstrated a wet response
showing the importance of freshwater flows to these types of
species in San Francisco Bay.

It also appears that outflow affects Bay shrimp abundance in
San Francisco Bay. Abundance indices for this species were
greater during wet years than during dry years. Preliminary
study results also have led to the conclusions that some fish
appear to be more widely distributed during wet years.

There are two reasons why fish may change their
distribution. First of all, they may change distribution
because of salinity alterations. Salinity may increase or
decrease above or below species salinity preferences and cause
them to move to another area.

73

TABLE 2. Species response to water year type. Number in paren¬
theses is that fish's rank in the fifteen most abundant
species.

Wet Response
Fresh

Threadfin shad
Carp

Prickly sculpin

Anadromous

White sturgeon
Green sturgeon
Steelhead

Dry Response

Sacramento squawfish
Tuleperch

Pacific lamprey

Mixed Response

Inland silverside

Splittail

White catfish

American shad (14)
King salmon
Striped bass (5)

Estuarine

Threespine stickleback
Yellowfin goby (10)
Longfin smelt (2)
Staghorn sculpin (8)
Starry flounder (12)

Marine- estuarine

Pacific herring (3)
Cheekspot goby

Marine

Leopard shark
Pile perch

Speckled sanddab (7)
Diamond turbot
Sand sole
California tongue-
fish

Brown smoothound
Spiny dogfish
Pacific tomcod
Topsmelt
Showy snailfish

Arrow goby
Walleye surfperch (1)

Bat ray

Whitre seaperch
Jacksmelt (13)

Black perch
Rubberlip seaperch
Pacific butterfish
Boneyhead sculpin

Delta smelt
Bay goby (11)

White croaker (9)
Northern anchovy
Plainfin midshipman
(15)

Shiner perch (4)

Night smelt
Bay pipefish
Barred surfperch
Brown rockfish
Lingcod

English sole (6)
Dwarf perch
Big skate
Surf smelt
Curlfin turbot

74

Secondly, circulation patterns can affect the distribution
of the larval stages of many fish. Larval English sole distri¬
butions appear to reflect outflow related circulation changes.
English sole spawn offshore in the Pacific Ocean. Adult sole
usually do not occur in San Francisco Bay. The larvae spawned
offshore presumably are carried by gravitational circulation
into the Bay. The magnitude of that circulation is related to
the magnitude of Delta outflow. Data from 1980-1983 showed that
the distribution of larval sole (3-5 mm) was broader during the
high flow years than during the low flow year. During the year,
larval sole occurred only near the mouth of the Bay, near the
ocean, while during the high flows (1983) larvae were found
throughout San Pablo and South Bays.

Early study efforts also have found that large, freshwater
pulses move through the system in winter and spring and signifi¬
cantly lower salinity in this system. These salinity changes
affect fish distribution. As a rule, pelagic species (e.g.,
northern anchovy) normally found in the Delta, Suisun and San
Pablo Bays during dry periods move downstream after these
pulses. On the other hand, some bottom species (e.g., juvenile
English sole) usually found in Central Bay move upstream during
these events.

It also has been found that flow altered distributions of
certain species result in increased abundance of these species.
For example, a major cause of the year-to-year variation in
abundance of Crangon shrimp appears to be survival of the early
life stages (i.e., the larvae or juvenile), not to the number of
reproductive females present. It has further been found that
distribution of the adults that is affected by the flows varies
between the years. In wetter years, the reproductive population
is further downstream near the Golden Gate. The survival of the
juveniles is much higher there. It appears that flow affects
distribution of adults, which in turn sets abundance for the
year because more juveniles survive.

Future Project Needs

The above provides a quick, general summary of the
accomplishments of the Interagency Program and the findings of
the Delta Outflow Study, in particular. The remainder of this
review will emphasize future project needs.

In order to ensure protection of San Francisco Bay
resources, various things are needed. More information on water
quality or pollution impacts on fishery resources in the Bay is
desperately needed. The Delta Outflow Study has documented flow
related effects, but little is being done to determine effects
of various waste discharges on fish and shrimp. Once again this
points to a division of study effort. One effort to study
pollution in the Bay by the Aquatic Habitat Institute is being
planned, but without strong local or Federal financial support,
this program will not be productive.

75

Other scientific needs exist and the Delta Outflow Study
will be fulfilling these needs in the future. For example, the
study has discovered some of the qualitative relationships
between fishery resources and freshwater flows, but these re¬
lationships must be confirmed and quantified. In other words,
how much of a population reduction or increase results if
outflows are reduced by some amount? Reported amounts of
reduction in other systems that have caused adverse responses
range up to approximately 47 percent. In an average rainfall
year, approximately 50 percent has been diverted from San
Francisco Bay. The study also must develop some predictive
capability, through simple fishery models, to be used when the
regulatory agencies eventually set protective standards.

The Outflow Study also will need to document relationships
between fishery resources and circulation/hydrodynamic patterns.
Some organisms use circulation processes for transportation of
their young, but the quantitative relationships between outflows
and these processes are unknown. Beyond that, it must be deter¬
mined whether any observed flow-related circulation changes will
impact those organisms known to use currents in the Bay and if
so, whether or not such impacts will be detrimental.

Policy needs for San Francisco Bay center around two
issues. First, in California a long standing controversy re¬
garding the role of the Federal Central Valley Project in
protecting beneficial uses has been debated. This issue has
recently been resolved to the state's satisfaction in the
Coordinated Operations Agreement (COA). Congress must act on
this Agreement. Second, continued funding support from the USBR
to continue the outflow studies is desperately needed. Study
contracts are renewed each year and, from time-to-time, the
project has been threatened due to budget cuts in the Bureau
program. Long-term, financial support is needed to continue
these important studies.

In conclusion, California is a divided state, but through
agency coordination and cooperation, and also some sound
scientific studies, progress is being made toward protecting
and, in fact, in some cases, enhancing fish and wildlife
resources.

76

THE IMPACTS OF ESTUARINE DEGRADATION AND CHRONIC POLLUTION
ON POPULATIONS OF ANADROMOUS STRIPED BASS (MORONE SAXATILIS)
IN THE SAN FRANCISCO BAY-DELTA. CALIFORNIA:

A SUMMARY

Jeannette A. Whipple, R. Bruce MacFarlane
Maxwell B. Eldridge, and Pete Benville, Jr.
Tiburon Fisheries Laboratory
NOAA/National Marine Fisheries Service

Introduction

When most of us think of pollution effects on the marine
environment, we are likely to think of dramatic events such as
major tanker accidents and oil spills, or fish kills resulting
from sewage effluents and toxic spills. These incidents are
highly visible and receive considerable public attention. There
is no doubt that such occurrences are damaging to the marine
environment and warrent concern about the protection of that
environment.

Unfortunately, we may be deluded into thinking that if we
prevent or ameliorate damage from such catastrophic events, our
pollution problems have been solved. If we do this, we overlook
a potentially greater problem -- that is continual or chronic
input of pollutants at lower levels. For example, in the 1960s,
there was considerable activity leading to decreased sewage
pollution of San Francisco Bay. This was certainly commendable,
but also led to the impression that our pollution problems were
over. Little attention was paid to the less visible and poten¬
tially more harmful effects of increasing pollution from "water-
soluble" chemicals.

The long-range effects of chronic exposure to pollutants on
our aquatic resources are still relatively unknown. Levels of
pollutants, in this situation, are lower but more prevalent.
Effects, if they occur, are more subtle, yet the damage to our
resources may be considerable and, in many cases, irreversible.

It is difficult to study effects of chronic pollution for a
number of reasons. First, most marine ecosystems potentially
impacted by pollutants are inherently complex and variable in
space and time. Many ecosystems are described incompletely,
either qualitatively or quantitatively, and even under com¬
pletely natural conditions. Natural perturbations may exceed
those induced by man's influence. For example, in 1983 the El
Nino off the coast of California resulted in warm water
conditions and significant alterations in distribution and
survival of coastal fishes. This makes it very difficult to
detect alterations in the environment ascribable to pollution,
and even harder to predict them.

77

A second difficulty arises from the complex array of dif¬
ferent pollutants occurring in the marine environment, parti¬
cularly in estuarine ecosystems such as San Francisco Bay- Delta,
which are most affected by man.

Finally, sublethal effects of low pollutant concentrations
on organisms are subtle and difficult to quantify on an indi¬
vidual or population level; their detection also may be obscured
by inherent species variability such as age, sex, or genetic
differences.

A solution to this intricate problem requires a long-term,
cooperative effort. The goal of the Physiological Ecology
Investigation at Tiburon Laboratory has been to contribute to an
understanding of the long-term ecological consequences of
pollutant effect on aquatic resources. Specifically, we were
concerned with developing knowledge of effects of chronic
low-level pollutants on fisheries. Although the understanding
of fate and effects of pollutants in the marine environment has
increased in the past 20 years, this knowledge is still limited
primarily to acute effects of single pollutants or pollutant
classes. Little is known of chronic, interactive effects of pol¬
lutants within and between pollutant classes. Most effects
studies are limited to the laboratory; little information exists
on the quantitative effect of pollutants on a population level.
Finally, few studies address the interactions of pollutants with
inherent characteristics of the species or with other environ¬
mental factors.

In order to to describe source of variability in pollutant
effects on striped bass more completely, we used techniques of
multivariate analysis similar to those used in epidemiology. We
were then able to refine the data to determine the best methods
for measuring pollutant effects in both the field and in labora¬
tory experiments.

Our approach concentrated on "easy to measure" and/or "sensi¬
tive" characteristics of the organisms which appeared to cor¬
relate with pollutant burdens. Initially, the measurements were
on several levels -- from the biochemical to the subsample (popu¬
lation) level. After preliminary studies, the most sensitive
variables were delineated. Selected groups of variables
(factors) were then designated as measures of body conditions,
liver condition, and egg condition. Eventually, these factors
coefficients were translated into an overall assessment of the
health of the organism. The coefficients also can be used to
estimate quantitative effects on a population level, such as
reductions in growth, reproduction, and survival. Some of the
measurements are also more sensitive and consequently more
effective in giving us an early warning that individuals and/or
the population are stressed. Ultimately, we hope to synthesize
the results into a model of the impacts of long-term chronic
pollution on "natural" mortality rates and resulting changes in
the population of the affected fishery.

78

The following questions were asked when formulating our
research plans. In this summary, the questions are placed
within the context of the Office of Marine Pollution Assessment*
Research Program Conceptual Organization (Figure 1):

Anthropogenic Activities

1. Which pollutants are potentially impacting our marine
resources, including fisheries?

2. What are the sources of these pollutants?

Marine Ecosystem Processes

3. What are the interactive effects of the pollutants on
fishes? How are they related to other ecosystem pro¬
cesses, such as variation in outflow and diversion?

Consequences Attribute to Anthropogenic Activities

4. Are there effects on fish attributable to chronic pol¬
lutant exposures?

5. If so, what are the effects and which measurements pro¬
vide the most sensitive and specific assessment of
them?

6. Are the effects reversible? Are there either short¬
term or long-term irreversible effects on individuals
and populations?

Judgemental Processes

7. What are the quantitative reductions in populations in
growth, reproduction, and survival attributable to
pollutants?

8. Can these effects be predicted?

9. What recommendations based on our results can be made
to management and regulators for the decisions neces¬
sary to regulate anthropogenic activities deleteriously
affecting fisheries?

Other Compartments

10. Other compartments in the conceptual representation

Figure 1 are within the purview of management

*0MPA is now the Ocean Assessment Division of the National Ocean¬
ic and Atmospheric Administration (NOAA) .

79

Figure 1. Conceptual representation of Office of Marine
Pollution Assessment Research Program. From R.E. Burns,
January 19, 1982. "Office of Marine Pollution Assessment
(OMPA) Financial Assistance for Marine Pollution Research."

80

In June 1980, the Cooperative Striped Bass Study (COSBS)
team was organized to examine different aspects of the above
questions (Jung and Bowes, 1980; Jung et,. al. 1981; Whipple,
Crosby, and Jung, 1983; Whipple et. al. 1984; Jung, Whipple, and
Moser, 1984).

At the Tiburon Laboratory, we concentrated on the affects of
pollutants on striped bass populations (4 through 8, above).

From this research, a number of recommendations have been made
(9 above). The State Water Resource Control Board (SWRCB)
stressed work on the anthropogenic sources of pollutants found
in the striped bass and identification of the pollutants (1 and
2 above), funded additional studies on effects of pollutants and
parasites, (4 through 8), and took a number of management ac¬
tions (10 above). The California Department of Fish and Game
(CDFG) also participated in management decisions (10 above).

There were a number of excellent reasons for selecting the
striped bass as a model species in the San Francisco Bay- Delta
ecosystem. The striped bass is a long-lived fish (approximately
2 0 years) and at all ages appears to accumulate relatively high
levels of pollutants. It is a tertiary carnivore and accumu¬
lates pollutants throughout the food chain. Striped bass are
also very euryhalone, occurring in offshore marine areas, estu¬
aries, and in freshwater. They occur on all coasts of the Unit¬
ed States and have been introduced in other countries. This
fishery is also of great commercial and recreational value.

The major reason for studying striped bass, however, was the
long-term decline on this population in the area, as well as in
most other estuaries of the United States. We suggest that at
least part of the decline may be because of the interactive dele¬
terious effects of anthropogenic factors, such as water
diversion and pollution.

California Department of Fish and Game (CDFG) biologists
have studied the striped bass population in the San Francisco
Bay- Delta estuary for about 40 years. Their work provided the
framework for studies of this species, particularly in the
field. The initial results of CDFG studies revealed a high cor¬
relation between outflow from the Delta and survival of striped
bass to "young-of-the-year" or juvenile stage. A correlation
also existed between the percentage of water diverted south
through the California aqueduct system and survival of juve¬
niles. On the basis of these correlations, CDFG was able for
some years to predict survival of juveniles and recruitment to
the fishery. These predictions became less reliable in later
years (since approximately 1975), although outflow and diversion
remain major controlling factors in survival. Figure 2A shows
the decline in survival to juvenile striped bass in both the
Suisun Bay and central Delta nursery areas; Figure 2B shows the
decline in adult striped bass (from Stevens et. al. 1985).

81

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83

Figure 2B. Two measures of adult striped bass population size;
change in Peterson and catch-per-unit effort estimates of adult
bass with year. Decline obvious from 1975. (Stevens et . al . , 1985)

The interaction of yearly temporal variation in net flow
with spatial variation in spawning and nursery habitats appeared
to be a major factor in the annual variation in survival of
striped bass. We hypothesized that in critically low water
years, or when certain pollutant "events", such as spills,
occurred during spawning migration, this spatial-temporal equi¬
librium was disturbed. When this happened, the effects of
pollutants and other environmental stress factors appeared to
play a larger role in contributing to the mortality of striped
bass. This system was thought of as a "model" for the inter¬
action of the anthropogenic stressors of water diversion and
pollutants.

To begin research, we derived the following specific goals:

1. To determine the consequences of chronic pollutants
impacting a fishery's population.

2. To use striped bass, an apparently declining population in
the San Francisco Bay ecosystem, as a "model species" for
such a study.

3. To compare the San Francisco Bay-Delta striped bass popula¬
tion to other populations less impacted and more impacted
by pollutants.

4. To determine the condition or health of striped bass
caught in the field, and if in poor condition, to deter¬
mine correlation with pollutant burdens in tissues.

5. To do laboratory studies to corroborate field-determined
correlations between fish condition and pollutant burdens.

6. To formulate a quantitative model showing relationships
between pollutants and the condition of the bass popula¬
tion in terms of reductions in growth, reproduction, and
survival.

7. To provide recommendations to appropriate agencies in¬
volved with management of fisheries, specifically, the
striped bass fishery, and to agencies responsible for the
maintenance of water quality and the health of marine
ecosystems.

8. To cooperate with other agencies in determining the main
sources of pollutants deleteriously affecting striped
bass.

9. To cooperate with other agencies in determining the pol¬
lutant burdens in striped bass potentially harmful to
human health.

84

10.

To cooperate with other agencies in determining the re¬
lationship of pollutant effects on striped bass to other
ecosystem processes, e.g., water outflow and diversion and
other species in the striped bass food chain.

11. To make field tests of predictive models.

The results here are updated from a previous report
(Whipple, 1984) and summarized from a manuscript in prepara¬
tion: "A multivariate approach to studying the interactive

effects of inherent and environmental factors, including pol¬
lutants, on striped bass in the San Francisco Bay- Delta, Cali¬
fornia" by Jeannette A. Whipple, R. Bruce MacFarlane, Maxwell B.
Eldridge, and Pete E. Benville, Jr.

Methods

We have examined approximately 500 fish captured in the
field from the San Francisco Bay-Delta (400); the Coos River,
Oregon (41); Lake Mead, Nevada (30); and from the Hudson River,
New York (26). Techniques of histopathological examination and
autopsy have been developed to assess the health of striped bass
and to continue annual monitoring (Whipple, et. al. 1984).
Approximately 350 characteristics of the fish were examined
initially -- from the biochemical level to organ system and in¬
dividual organism levels -- to determine the best measures of
health. Subsamples were taken of liver, ovaries and muscles to
determine burdens for the following major classes of pollutants:
petrochemicals or petroleum hydrocarbons (monocyclic aromatics,
polycyclic aromatics), chlorinated hydrocarbons (including PCBs,
toxaphene, DDT, and its metabolites and others), and heavy
metals (copper, iron, zinc, cadmium, mercury, lead, nickel, and
others). Tissues were also scanned for EPA's priority
pollutants.

Multivariate statistical techniques, including principal
component factor analysis (Nie, 1975), were applied to the field
data to determine correlations between sets of variables describ¬
ing conditions and the pollutant burdens. The following summary
of results includes correlations and regressions found signifi¬
cant in multiple regression analyses at the P < .05 level or
less. Several laboratory experiments were performed to verify
correlations seen in field fish (Jung, Whipple, and Moser,

1984).

Results and Discussion

The following summary of specific results apply to the
goals above:

1. Location. There were differences among locations. The

greatest proportion of the variability was attributable to
different sampling locations. Thus, factor analyses were
separated by location before assessing the other vari¬
ability.

85

o

Fish from the San Francisco Bay-Delta estuary were in
poorer health or condition than fish from the Coos
River, Oregon. A 1982 sample indicated that Hudson
River fish were also in better health than those from
the San Francisco Bay-Delta.

o Comparisons with samples from Lake Mead, Nevada

showed that fish from Lake Mead were definitely less
parasitized and had lower pollutant burdens than
those from the San Francisco Bay- Delta system. Lake
Mead fish, on the other hand, had poor body condi¬
tion, indicating starvation and insufficient food.

o Fish from the San Francisco Bay- Delta had higher

tissue concentrations and a greater number of sepa¬
rate petrochemical compounds than did those from the
Coos River, Oregon or the Hudson River, N.Y., except
for some xylenes, which were relatively high in all
populations of fish sampled.

o Fish from the Coos River had the lowest concentra¬
tions of chlorinated hydrocarbons and heavy metals.

o Fish from the Hudson River had higher concentrations
of PCBs in gonads and muscle, and higher concentra¬
tions of chlordane and dieldrin in gonads than did
San Francisco Bay- Delta fish.

o Fish from the San Francisco Bay- Delta had higher
levels of copper, zinc, cadmium, and nickel in
gonads; higher levels of copper, zinc, mercury, and
nickel in liver. Hudson River fish had higher levels
of mercury in gonads and muscle and higher cadmium in
liver.

o Lesions caused by host reactions to cestode or

tapeworm larval parasites (Lacistorhvnchus tenuis)
were found only from the San Francisco Bay- Delta.

The concentrations of several other types of
parasites were also higher in fish from the San
Francisco Bay- Delta area than in fish from any other
area. Hudson River fish had a totally different
parasite assemblage than fish from the West coast.

o Egg condition in fish from the San Francisco Bay-

Delta was significantly poorer than in fish from any
other area sampled.

o Fish from San Joaquin River were in poorer condition
than those from the Sacramento River, showing de¬
creased body condition, higher levels of cestode
larvae, and higher concentrations of zinc and other
metals.

86

o

Results show that it is difficult to find a "control
population" for comparison with the California popu¬
lation because all examined so far have been impacted
in some way by pollutants and/or have significant
environmental differences. Nevertheless, of all popu¬
lations examined, the San Francisco Bay/ Delta fish
appear in the worst health.

2. Sex. Although most fish sampled were females, both sexes
were impacted. Because sexes were sampled differently,
and because of strong sexual differences, sexes were also
separated in the factor analysis.

o Males had higher levels of petrochemicals and PCBs in
the liver and primarily toluene in testes.

o Females had higher levels of petrochemicals in

ovaries, higher levels of metals in all tissues and
higher levels of PCBs in ovaries than males had in
testes.

o Body and liver condition was poorer in males than in
females.

3. Other Factors. After location and sex, a large proportion
of the variation (in the selected variable data base) was
accounted for by the factors of age, color pattern, sexual
maturity, pollutants, year, the time in the prespawning
season, and parasites. An example of factor analysis
results is given for the San Joaquin River from 1978-1983
Table 1.

o Year. Concentrations of petrochemicals varied with
year (1978 to 1984) of sampling (Table 2). Most
separate compounds and higher levels were found in
striped bass in 1978, 1979, and 1981. Some fish from
all years, however, contained petrochemicals (except
small sample of 7 fish in 1982). Cestode larvae and
lesions varied yearly and related to age and sexual
maturity of adults. Egg condition was poorest in
1978, 1979, and 1981, correlating significantly with
petrochemical concentrations in the liver and ova¬
ries.

o Age. Older fish were in poorer condition, with
reduced fecundity, higher parasites loads, and
greater concentrations of some pollutants,
particularly PCBs and metals.

o Color pattern type. There were different growth and
reproduction rates, body proportions, and pollutant
and parasite burdens in fish of different color
pattern type (e.g. solid-striped, broken-striped,
etc.) .

87

Table 1. -- Factor analysis results for prespawning striped bass.
Proportion of variance in data base accounted for by different factors,
or sets of variables. San Joaquin River prespawning females (n=157
fish); 1978-1983. The names of factors indicate the major controlling
variables in factor sets.

PROPORTION OF VARIANCE
FACTOR % ACCUMULATIVE %

1

AGE, WET WEIGHT

10

10

2

COLOR PATTERN -GENERAL

9

19

3

SEXUAL MATURITY

8

27

4

PETROLEUM HYDROCARBONS:

(Gonad & Liver -o-Xylene )

7

34

5

YEAR

6

40

6

CHLORINATED HYDROCARBONS:

(Gonad & Liver-PCB’s)

5

45

7

CHLORINATED HYDROCARBONS:

( Gonad & Liver-DDT )

5

50

8

TIME, TEMPERTURE

4

54

9

PARASITES-CESTODE LESIONS

4

58

10

YEAR

3

61

11

METALS : Liver- ( LSI )

3

64

12

PETROLEUM HYDROCARBONS:

( Gonad-Ethylbenzene , m-Xylene )

3

67

13

SEXUAL MATURITY

3

70

14

PETROLEUM HYDROCARBONS :

( Liver-Ethylbenzene ,

1 , 2-Dimethylcyclohexane )

2

72

15

BODY CONDITION

2

74

16

PETROLEUM HYDROCARBONS :

2

7 6

(Liver-Benzene, m-Xylene,

_ 1 . 2-Bimvlcyclohexane ) _

INHERENT FACTORS ENVIRONMENTAL FACTORS UNIDENTIFIED

NATURAL FACTORS POLLUTANT FACTORS
32% 17% 27% 24%

FACTOR

NO. FACTOR NAME

88

Table 2. Year factor; ranked differences among years in inherent
characteristics, environmental variables and condition of striped bass.
Based on factor analyses of prespawning female striped bass collected from
April to June; San Joaquin River. Loadings on factors greater than or
equal to 0.30. Ranked from highest (1) to lowest (7) total mean values.

NS = not sampled; NM = sampled, but not measured.

YEAR1 1978 1979 1980 1981 1982 1983 19842

<N) (59) (42) (21) (12) ( 7) (16) (21)

VARIABLE - - - - - - -

Inherent Factors

Age

2

4

7

1

3

6

5

Color Pattern

6

3

1

5

4

2

2

(Stripe Breakage)

(8.5)

(9.9)

(10.5)

(9.0)

(9.1)

(10.1)

(10.1

Environmental Factors

Outflow

4

5

3

5

2

1

?

Diversion

2

1

2

1

3

4

?

Petroleum HC-

Monocyclic Aromatics;

Gonad

4

2

5

1

6

3

NM

Liver

Petroleum HC-

3

5

6

1

4

2

6

Alicyclic hexanes

Gonad

3

2

5

3

5

1

5

Liver

3

2

5

4

5

1

5

Metals-Gonad

Copper

1

NS

3

2

NM

NM

NM

Zinc

2

NS

3

1

NM

NM

NM

Metal s-Liver

Copper

NS

NS

3

2

NM

NM

1

Zinc

NS

NS

3

2

NM

NM

1

Cadmium

NS

NS

NS

2

NM

NM

1

Chromium

NS

NS

NS

1

NM

NM

2

Mercury

NS

NS

NS

1

NM

NM

2

Selenium

NS

NS

NS

2

NM

NM

1

Parasites

Tapeworm Larvae

6

5

2

6

1

4

3

Tapeworm Lesions

4

1

3

2

5

1

4

Tapeworm Rafts

6

1

4

5

6

3

2

Total Parasite3
Severity

2

2

5

4

1

4

3

Condition Factors

♦Egg Resorption

1

2

4

2

6

3

5

(More resorbed eggs and

ovaries

and abnormalities

, less

delayed

maturation) .

1 Sample sizes in

1981

and 1982

were small because of reduced populatic

size of prespawning adults.

2 Some outflow and diversion data

3 All types of parasites and host

not available,
reactions .

89

o

Sexual Maturity. Spent females were significantly
different than maturing females in having higher con¬
centrations of petrochemicals in the liver (parti¬
cularly toluene) and higher parasite burdens. Young
prespawning females exhibited more alterations of egg
maturation rate and resorption associated with petro¬
chemicals. Young prespawners were also more likely
to have open or only partly healed cestode lesions.

o Parasites. A significant proportion of adults

(approximately 33 percent had scars from cestodes-
induced lesions. These fish were in generally poorer
condition than those without scars, and had higher
levels of pollutants, particularly petrochemicals.

Young adults and juveniles showed open lesions from
these parasites (Figure 3). Many of the older fish
had relatively large numbers of Anasakid roundworm
larvae, sometimes in muscle. This worm can impact
the health of man.

4. Pollutants. Adult striped bass from the San Francisco Bay-
Delta system contained relatively high levels of pol¬
lutants from several classes (Table 3. ranges; Whipple,
et. al. in prep, contains all means and standard devia¬
tions). Some of these pollutants showed strong
correlations with poor health and condition, parasite
burdens and impaired reproduction.

o Petrochemicals. There were significant levels of

monocyclic aromatic hydrocarbons, including benzene,
toluene, ethylbenzene and three isomers of xylene, in
tissues of striped bass. There were also significant
levels of alicyclic hexanes. All these components
are relatively toxic to fish (Benville and Korn,

1977; Benville et. al. 1985). In addition to the
effects on the fish associated with these compounds
in liver and ovaries, the muscle tissue appeared to
differentially accumulate toluene which has been
shown previously to cause the "tainting" or bad fla¬
vor in other species. Other data (Vassilvos, et. al.
1982) show that there were also relatively high lev¬
els of polycyclic aromatics in adult striped bass.

For example, levels of thiophenes in fish from the
San Francisco Bay- Delta were higher than in fish from
other areas. These compounds are carcinogenic.

High levels of petrochemicals in the fish correlated
strongly with deleterious effects measured, including
egg resorption (Figure 4) and abnormal reproduction.
The mean egg resorption by year, comparing locations,
is shown in Figure 5. In 1982, sample size (7) was

90

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Ti 0 0
0 -P M 0

P-I o

■H O

0 -P • tn
-P 0 0
0 tn O -H
0 -H £
03 -H -P O
0 -P O ,0

0 o a.) 0
0 0^

•H 0 0 0
0 0 -rH 0
0 I 0
10 0 H O
0 0 0
K> -H

• O 0 >i
ro 0 r-H

0 -P 0
0 0 O O
0 -H 0
0 10 0 01
Cd -p

•H M-| >,-h
0 0 0 3:

91

Figure 4A. Eggs from ovaries of striped bass.
Normal eggs in secondary to tertiary yolk stage.

92

Figure 4E. Abnormal eggs, in varying stages of
resorption. This condition is associated with
petrochemicals .

93

Figure 4C. Abnormal eggs, in late development stage,
being resorbed. Note dark areas of melanin-containing
melanomacrophages in intercellular areas. This
condition is associated with DDT.

94

REPRODUCTION: PERCENT EGG RESORPTION

30

Percentage
of Eggs 20
Resorbed

10

I

1978 1979 1980 1981 1982 1983 1984
i - San Joaquin River - 1

Location / Year

1980 1982

Coos Hudson
River River

Figure 5. Mean egg resorption in striped bass
prespawning females by year (1978-1984) and at
different locations.

95

too small for a representative assessment. An ex¬
ample of the proportion of egg resorption because of
various factors, including petrochemicals, is shown
in Figure 6. Reduced egg condition was particularly
associated with high concentrations of ethylbenzene
and 1, 2-dimethylchyclohexane. These components are
also among the more toxic and persistent in tissues
of the low-boiling point petrochemicals.

High concentrations of benzene were associated with
blood cell destruction, abnormal blood cell develop¬
ment and other blood parameters. There was also a
correlation between the presence of lesion scars and
petrochemical concentration, particularly toluene and
ethylbenzene.

Concentrations of monocyclic aromatics in the tissues
of field fish correspond to levels reached in tissues
of fish exposed in the laboratory to 50-100 ppb mono-
cyclics (particularly benzene). The bioaccumulation
was generally about ten times higher than the water
concentrations (Whipple, et. al. 1981).

o Chlorinated hydrocarbons. There were relatively high
levels of PCBs, DDT, and its metabolites, and other
chlorinated hydrocarbons, including toxaphene, in
liver and gonads and fish from the San Francisco Bay-
Delta estuary (Table 3). Concentrations of some
chlorinated hydrocarbons were at levels resulting in
deleterious effects in other fish (Jung, Moser, and
Whipple, 1984). The presence of DDT in liver and
gonads (not metabolites DDD and DDE) was associated
with abnormal egg development and necrosis of eggs
(Figure 4C). Delayed egg maturation rates (vitello¬
genesis) were associated with PCBs in ovaries.

o Heavy metals. There were relatively high levels of
zinc and copper and other metals in adult striped
bass livers and gonads (Table 3). The concentration
of zinc and other metals correlated with decreased
body and liver condition in some fish. Cadmium,
nickel, zinc, and copper also correlated with reduc¬
tions in egg viability in the 1981 San Joaquin River
sample. High levels of other metals were found,
particularly mercury, in some fish.

o Pollutant interaction. Initial results show pol¬
lutants interacted in affecting the fish. In parti¬
cular, high levels of petroleum hydrocarbons inter¬
acted with chlorinated hydrocarbons to produce ef¬
fects on reproduction. Data also show that hydro¬
carbons and metals interact to produce deleterious
effects on egg and liver condition.

96

Figure 6. Proportion of total variance in egg
condition (egg resorption) accounted for by different
factors. Derived from factor equations in factor
analysis. Most fish collected in this year had high
levels of monocyclic aromatics in the liver and gonads.

EXAMPLE: San Joaquin River; 1978. N=59 females.

+EGG RESORPTION = . 35F3 = .42F6 = . 54F11 = .42F13 = U

U = Unidentified Variance; DMCH = 1 , 2 , -dimethy lcyclohexane
EGG STG. = Egg Stage; EBZ = Ethylbenzene; CU = Copper;

COL PAT = Color Pattern; TOL = Toluene.

97

Table 3. — Concentration ranges of selected pollutant classes from the San
Francisco Bay-Delta estuary; data available to present. Tissue data from
adult prespawning striped bass (Morone saxatilis) . Tissue concentrations
in ug/g (ppm) wet weight hydrocarbons ug/g (ppm) dry weight for metals.

Data from this study and Vasillaros et al. (1982), Eaton (1975), and Girvin
et al • (1978) . ND = not detectable; NM = not measured.

Concentration

in water Concentration in tissues (ppm)
(dissolved)

Pollutant class_ uer/L (ppb) Liver Gonads Muscle^

Petroleum hydrocarbons

Total monocyclic aromatics

1-200

0.01-10

0.01-10 (

). 01-7. 52

Total alicyclic hexanes

ND

0.02-5.0

0.02-10

0

Total polycyclic aromatics

(All components)

o

— Whole fish composite

10.0 -

Total naphthalenes (Dicyclics) ?

— Whole fish composite

0.009 -

Total sul fated thiophenes

o

— Whole fish composite

6.0 -

Chlorinated hydrocarbons

DDT

ND

0.09-0.12

0.10-0.68

NM

COD

ND

0.10-0.98

0.13-2.8

NM

DDE

ND

0.03-3.1

0.10-12

NM

Toxaphene

0.03-0.32

o

•

0.20-2.0

NM

Total PCB's

ND

0.25-13

0.81-13 (

). 20-4.0

Trace metals

Cadmium

0.08-0.20

0.29-9.4

0.08-0.71

0.18-1.3

Chromium

ND

0.61-3.3

0.51-2.2

0.31-2.2

Copper

1-4

1.0-220

1.0-35

0.10-12

Lead

0.03-0.12

0.09-0.37

0.06-0.89

0.11-0.62

Mercury

ND

0.49-13

0.03-0.96

0.06-1.6

Nickel

1-6

0.60-1.8

0.37-2.1

0.50-2.0

Selenium

o

•

3.2-21

NM

NM

Zinc

2-6

7.0-250

3.0-310

1.0-66

1Muscle analyses with no skin attached. Mostly toluene in muscled

98

Pollutants most implicated in deleterious effects on
fish are, in order: ethylbenzene, 1, 2-dimethylcyclo-
hexane, benzene toluene; DDT, copper, zinc, cadmium,
nickel, and mercury. However, other pollutants may
be involved that we were unable to measure. For ex¬
ample, recent measurements show that there are rela¬
tively high levels of selenium in liver and gonads of
striped bass. Several pollutants, particularly chlo¬
rinated hydrocarbons, polycyclic aromatics, cadmium,
and mercury were found at levels sufficiently high
not only to affect the health of the fish but also to
potentially affect human health.

The relevant fact is that there are strong associa¬
tions of these pollutants with decreased condition,
growth, reproduction, and possibly survival of
striped bass.

5. Laboratory experiments. Experiments performed in the

laboratory showed that representative pollutants (benzene
and zinc) produced effects similar to those observed in
the field (Jung, Whipple, Moser, 1984; Whipple, et. al. ms
in prep.). Laboratory exposures equivalent to high chron¬
ic water levels in the field resulted in tissue concen¬
trations similar to those in field fish (magnitude of
concentration of benzene and/or other total MAH was ap¬
proximately 10X). The effects on condition of tissues and
organs, and other parameters were also similar. The fol¬
lowing were some major results:

Adults:

o Benzene induced egg resorption in prespawning females
similar to that in field fish. Fish with higher
pollutant burdens when exposed to benzene were most
seriously affected.

Juveniles:

o Uptake of benzene and zinc appeared to be antagonis¬
tic -- high concentrations of benzene in the liver
were correlated with low concentrations of zinc.

o Benzene appeared to accelerate and increase the
inflammatory response to roundworm larvae.

o Benzene was correlated with blood cell destruction

followed by increased production of immature red and
white blood cells.

o Zinc was correlated with decreased liver condition
(LSI).

99

Zinc was correlated with decreased levels of serum
proteins hypothesized to be immunoglobulins.

o Fish exposed to benzene or zinc had higher levels of
protozoan gill parasites than controls.

o The effects of benzene and zinc together resulted in
greater effects on the fish than either pollutant
alone, including the following:

Inflammatory response to parasitic worms was
accelerated.

Blood cells and serum proteins were more
deleteriously affected.

Liver tissue was more deleteriously affected.

6. Population Effects. Although influences other than

toxic chemicals (e.g, Delta outflow, larval food supply
and entrainment; Stevens et. al. 1985) also are involved
in the decline of the striped bass fishery, the fol¬
lowing hypotheses were also supported by the study
findings.

o There has been a reduction in numbers of larvae to
young-of-the-year juveniles. Laboratory studies
showed that larvae accumulate high levels of toxic
pollutants (e.g., benzene) with deleterious effects
(Eldridge et. al. 1981). These studies should be
corroborated in the field. We suggest that toxic
pollutants and parasitic cestode lesions may also
increase mortality of juveniles and subadults.

o There has been a reduction in the number of

spawning adults. The poorer condition of older
adults is at least partially due to the combined
effects of parasitism and pollutants. It is also
likely that increased mortality of adults has
occurred, leading to fewer older fish that normally
have the highest fecundity. Ultimately, this will
lead to decreased egg production by the population
and decreased abundance of juveniles. According to
Stevens et. al. (1985), this is probably an impor¬
tant cause of the decline in the striped bass popu¬
lation.

o The reduction in the number of eggs (fecundity) per
spawner, due to the combined effects of pollutants
and parasitism, was at least 36-50 percent in 1978.
This reduction was assessed from measurements of:

- delayed rate of maturation (vitellogenesis)

100

partial egg resorption

complete egg resorption in maturing ovary
no ovarian maturation in sexually mature fish
egg death

- reduction in number of eggs (fecundity)

Pollutants, therefore, can lead to additional decreases
in the egg production of the population. Additional delayed
mortality may have occurred in embryos and larvae after
spawning, resulting in even further reduction in survival.

o Multiple regression analyses were done with data

collected for the years 1978 to 1984 (7 years) from
San Joaquin and Sacramento Rivers. Results showed
that survival to young-of-the-year related to age
distribution of spawning adults, outflow and diver¬
sion, petrochemicals and egg resorption. The best
correlation was with egg resorption (Figure 7).

The hierarchy of relationships is probably as fol¬
lows (Figure 8): Environmental factors such as
lower outflow are associated with higher petrochemi¬
cal contmination; higher residues of petrochemicals
interact with inherent factors in prespawning
adults to affect condition and reproduction.

Greater egg resorption occurs and subsequently
there is higher larval mortality. Higher mortality
of eggs and larvae results in lower abundance of
juvenile striped bass. The important result, in
terms of fisheries management, is that recruitment
to the fishery is reduced. If successful, this
method can lead to the forecasting of recruitment
several years in advance. Our results so far,
however, are for a short period (7 years) and need
to be validated by continued monitoring before
conclusions can be drawn.

Conclusions

The San Francisco Bay- Delta estuary has been modified in
several ways since humans settled this area (Nichols et. al.
1986). Among the most significant of these is the elimination
of habitat for fish and other biota through human activities
such as filling of wetlands and diversion of water for agricul¬
ture. Further degradation of this estuary due to increased
diversion of water and increased disposal of toxic wastes is
predicted.

101

LOGe YOY SUISUN

36-

o

o SJ=SAN JOAQUIN RIVER
• SC=SACRAMENTO RIVER

3.4-

3.2-

30-

2.8-

2.6-

o

2.4-

0

T - 1 - 1 - 1 - 1 - 1 - 1 - 1

1.0 2.0 3.0 4.0

LOGe ARCSINE % RESORPTION

Figure 7. Correlation of yearly mean survival to young-
of-the-year juveniles (YOY) with mean egg resorption in
adult females of that spawning season. Data on YOY striped
bass index from David Kohlhorst

In YOY Suisun = 3.60 - .341 In Egg Resorption

r = - . 869; Pc. 001

102

POPULATION LEVEL EFFECTS

Figure 8. Population level effects. Determining
the relationship of environmental factors (e.g.
pollutants) on fish condition, reproduction and
recruitment to the fishery.

103

The striped bass population is a major component of the
San Francisco Bay- Delta estuary, particularly in past years
prior to its decline. It would be of interest to do more re¬
search on the relationship of the population dynamics of this
species to the flow dynamics of the estuary, and to examine
the striped bass in an ecosystem context. This would be of
critical importance in making future decisions on water
quality and the management of fisheries in the San Francisco
Bay- Delta system.

In conclusion, we believe that further investigation of
sources and effects of pollutants on striped bass and other
biota in the San Francisco Bay-Delta is warranted. We believe
also that enough is known for managers and regulators to act
now and that any activity reducing the input of these toxic
pollutants into the estuary will be beneficial to the health
and abundance of the striped bass population.

Acknowledgements

This research was supported by the National Marine
Fisheries Service and by a contract from the former Office of
Marine Pollution Assessment under the Marine Protection,
Research and Sanctuaries Act of 1972 (P.L. 92-532; Title II,
Section 202). Further cooperation and support was from the
State of California Water Resources Control Board within the
Cooperative Striped Bass Study, codirected by Marvin Jung,
Consultant. We appreciate the advice, assistance, and
cooperation of staff from the CDFG in Stockon, California,
particularly Donald Stevens and David Kohlhorst.

References

Benville, Pete E., Jr. and Korn, Sid, 1977: The acute

toxicity of six monocyclic aromatic crude oil components
to striped bass (Morone saxatilis) and bay shrimp
( Crangon francoscorum) . Calif. Fish and Game
63(4) :204-209.

Benville, Pete E. Jr.; Whipple, Jeannette A.; and Eldridge,
Maxwell B., 1985: Acute toxicity of seven alicyclic
hexanes to striped bass Morone saxatilis and bay shrimp
Crangon francoscorum. in seawater. Calif. Fish and Game
71(3) : 132-140.

Eaton, Andrew, 1979: Observations on the geochemistry of

soluble copper, iron, nickel, and zinc in the San Fran¬
cisco Bay estuary. Environ. Sci. and Tech. Res.

13(4) : 42 5-43 1.

Eldridge, Maxwell B.; Benville, Pete; and Whipple, Jeannette

A., 1981: Physiologic responses of striped bass (Morone
saxatilis) embryos and larvae to low sublethal concentra¬
tions of the aromatic hydrocarbons benzene. Proc. Gulf
Caribb. Fish Inst. 33:52-68.

104

Girvin, Donald C.; Hodgson, Alfred T.; Tatro, Mark E.; and
Anaclerio, Roy N. Jr., 1978: Spatial and seasonal
variations of silver, cadmium, copper, nickel, lead, and
zinc in south San Francisco Bay waters during two
consecutive drought years. Energy and Environ. Div.,
Lawrence- Berkeley Laboratory, University of California,
Berkely, CA. Final Report UCID-8008.

MacFarlane, R. Bruce and Whipple, Jeannette A., 1984: Striped
Bass Health Index. In-House report submitted to Advi¬
sory Committee for Aquatic Habitat Program, State Water
Resources Control Board. April, 1984.

Moser, Mike? Love, Milton? and Sakanari, Judy A., 1984:

Common parasites of California fish. Calif. Pep. Fish
and Game. 20 p.

Moser, Mike? Sakanari, Judy A.? Wellings, Sefton? and

Lindstrom, Kris, 1984: Incompatibility between San
Francisco striped bass, Morone saxatilis (Walbaum), and
the metacestode, Lacistrohvnchus tenuis (Beneden 1858).

J. Fish Pis. 7:397-400.

Moser, Mike? Sakanari, Judy A.? Reilly, Carol A.? and Whipple,
Jeannette, 1985: Prevalence, intensity, longevity, and
persistence of Anasakis sp. larvae and Lacistorhvnchus
tenuis metacestodes in San Francisco striped bass. NOAA
Tech. Rpt. NMFS 29: 4 p.

Nichols, Frederick H.? Cloern, James E.? Luoma, Samuel N.? and
Peterson, David., 1986: The modification of an estuary.
Science. 231:567-573.

Nie, Norman H.? Hull, Hadlai? Jenkins, Jean G? Steinbrenner,
Karin? and Bent, Dale H., 1975: SPSS: Statistical
Package for the Social Sciences, second edition.
McGraw-Hill, N.Y. 675 p.

Stevens, Donald E.? Kohlhorst, David W.? Miller, Lee W.? and
Kelly, D.W., 1985: The decline of striped bass in the
Sacramento-San Joaquin estuary, California. Trans. Am.
Fish. Soc. 114:12-30.

Vassilaros, D.L.? Eastwood, D. A.? West,W.R.? Booth, G.M.? and

M.L. Lee, 1982: Determination and bioconcentration of
polycyclic aromatic sulfur in heterocycles in aquatic
biota. In M. Cooke, A.J. Dennis, G.L. Fisher (editors).
Sixth international symposium for polynuclear aromatic
hydrocarbons: Physical and biological chemistry, p.
845-857. Battelle Press, Columbus, Ohio.

105

Whipple, Jeannette A.; Eldridge, Maxwell B.; Benville, Pete,

Jr., 1981: An ecological perspective of the effects of
monocyclic aromatic hydrocarbons on fishes. In F.J.

Vernberg (editors), Biological Monitoring of Marine
Pollutants, p. 483-551. Academic Press, N.Y.

Whipple, Jeannette A. 1982: The impact of estuarine degrada¬
tion and chronic pollution on populations of anadromous
striped bass (Morone saxatilis) in San Francisco Bay-
Delta, California. Annual research report submitted to
NOAA, OMPA. May 15, 1982.

Whipple, Jeannette A. 1984: The impact of estuarine degrada¬
tion and chronic pollution on populations of anadromous
striped bass (Morone saxatilis) in San Francisco Bay-
Delta, California. A summary for managers and regula¬
tors. NOAA, NMFS, SWFC Admin. Rpt. T-84-01, 41 p.

Whipple, Jeannette A.; Bowers, Michael; Jarvis, Brian; and
Moreland, Sharon, 1983: Report on the condition and
health of May 1982 sample of Hudson River adult, pre¬
spawning striped bass. In-house report, NMFS, Tiburon
Laboratory. 23 p. (Manuscript in preparation for publica¬
tion) .

Whipple, Jeannette A.; Jung, Marvin; MacFarlane, R. Bruce; and
Fischer, Rahel, 1984: Histopathological manual for
monitoring health of striped bass in relation to pol¬
lutant burdens. Tech. Mem. NOAA-TM-NMFS-S W FC-46, 81 p.

Cooperative Striped Bass Study (COBS) Reports:

Jung, Marvin and Bowes, Gerald, 1980: First progress report
on the Cooperative Striped Bass Study (COBS). Calif.

State Water Resour. Control Board. Sacramento, CA., 64 p.

Jung, Marvin, Whipple, Jeannette A., and Moser, L. Michael,

1984: Summary report of the Cooperative Striped Bass Study

(COSBS). A study of the effects of pollutants on the San
Francisco Bay- Delta striped bass fishery. Draft summary
report submitted to the California State Water Resources
Control Board.

Whipple, Jeannette A. and Jung, Marvin, 1981: Cooperative

Striped Bass Study (COBS). Appendix I: Procedures for
histopathological examinations, autopsies and subsampling
of striped bass. Calif. State Water Resour. Control Board,
Sacramento, CA., 46 p.

Whipple, Jeannette A.; Crosby, Donald G.; and Jung, Marvin,

1983: Third progress report: Cooperative Striped Bass

Study (COBS). Calif. State Water Resour. Control Board,
Sacramento, CA., 208 p.

106

SUBLETHAL EFFECTS OF CONTAMINANTS ON THE METABOLISM OF

METALS AND ORGANIC COMPOUNDS IN THE BAY MUSSEL

Florence L. Harrison and John P. Knezovich
Environmental Sciences Division
Lawrence Livermore National Laboratory
Livermore, CA 94550

Abstract

Biochemical mechanisms for the detoxification of metals and
organic compounds in the bay mussel Mvtilus edulis were
investigated. Mussels exposed to increased levels of copper in
the laboratory were shown to have proteins that bind and thereby
detoxify some metals. Chronic exposure to metals can cause
saturation of the detoxification system, however, and result in
metal interaction with sensitive enzymes and proteins. Accord¬
ingly, mussels from contaminated ecosystems (South San Francisco
Bay and near municipal outfalls in the Southern California
Bight) were shown to have increased levels of metals in meta¬
bolic pools as compared to mussels from a relatively pristine
ecosystem (Tomales Bay).

The ability of mussels to metabolize a trace organic
contaminant (o-toluidine) was defined. Mussels were shown to
metabolically activate this compound to a mutagenic form and
also to detoxify it via basal metabolic pathways. Mussels from
a contaminated site in San Francisco Bay demonstrated a dimin¬
ished ability to handle this contaminant as evidenced by a
overall reduction in metabolic rate. Continuing research on
mechanisms of biochemical adaptation will provide a better
understanding of the adaptive capabilities of mussels from
pristine and contaminated ecosystem.

Introduction

Organisms present in aquatic environments may be exposed
continually to low concentrations of a variety of metals and
organic compounds from anthropogenic sources. Concentrations of
these contaminants in the environment are generally below those
that cause mortality, but they may be sufficiently high to af¬
fect adversely an organism's growth rate, reproductive success,
or ability to compete with other species in the ecosystem.
Organisms may respond to such sublethal stress through the
evolution of reproductive, behavorial, and physiological strate¬
gies that confer biological resilience. The goal of our re¬
search is to understand the limits of adaptation of basic bio¬
chemical processes that confer resilience to aquatic organisms.
Our experiments are designed to obtain results that provide a
better understanding of the basic mechanisms used by aquatic
animals to handle increased quantities of trace metals and
organic compounds in the environment.

107

We focus on detoxification and biotransformation processes and
propose to develop methodologies that can be used to identify
aquatic ecosystems at risk, to evaluate ecosystem contaminant
capacity, and to monitor the impact of contaminants from waste
sites or effluent discharges.

Let us consider briefly changes in phsiological response
that fishes and invertebrates may undergo in response to
increases in environmental stress. These responses may be
divided into four phases: normal adjustment, which is
controlled by homeostatic processes; compensation, which is
maintained without significant cost to the individual;
breakdown, which occurs at the limit of compensatory processes;
and finally failure, which is characterized by irreversible
changes that result in death of the individual (Figure 1). Most
of the standards and criteria that have been set were based on
single species tests that used mortality as the endpoint.

Because concentrations that cause mortality are too high to
protect populations, standards and criteria were set not from
these values, but from LC50 values that were multipled by an
application factor considered to provide the degree of conser¬
vatism required. However, what may be more relevant for the
maintenance of healthy populations in aquatic ecosystems is the
setting of criteria and standards that are based on knowledge of
when the limits of compensatory processes are being approached.
This is critical because when these limits are exceeded, adverse
effects ensue.

The organism we chose to study was the bay mussel Mvtilus
edulis. This species was selected because it appears to have
evolved compensatory (adaptive) strategies that have resulted in
the distribution of mussels throughout the world in bays and
estuarine that have wide fluctuations in environmental condi¬
tions. Furthermore, there is an extensive data base on con¬
taminant levels in populations from pristine and polluted eco¬
systems (Goldberg et. al. 1978), and studies have been performed
to characterize its morphology (White, 1937) and its physio¬
logical and reproductive processes (Bayne et. al. 1976).

Metal Metabolism

Let us consider now metal metabolism in aquatic animals. It
has been well established that many aquatic animals accumulate
significant metal burdens from metal-contaminated ecosystems.
Although the biochemical processes associated with metal toxi¬
city have not been completely identified, specific effects have
been demonstrated. Evidence is available indicating that the
site of toxic action may be enzymes. However, the toxic effects
on enzymes may be mitigated by the organism's ability to detoxi¬
fy metals and eliminate them. It is apparent, then, that an
understanding of these toxification and detoxification processes
is required.

108

Normal adjustment Compensation Breakdown Failure

►

Figure 1. Changes in the physiological responses of aquatic animals to
increased levels of stress in aquatic ecosystems. Modified from Hatch (1962).

109

Toxification may result from alterations in enzyme acti¬
vity. These alterations may result when excesses of essential
metals or nonessential metals bind to enzymes. Metalloenzymes
may be rendered nonfunctional by conf irmational changes brought
about by binding with metals possessing properties different
from the metals that are required for optimal activity of the
metalloenzymes. Also, nonfunction may be due to induction of
conformational changes so that substrate molecules no longer fit
into binding sites. Alternatively, nonfunction could result
from splitting of enzymes into subunits, which could interfere
with feedback control mechanisms. Because any of these reac¬
tions could result in impaired metabolic activity, it is not
unexpected that adverse effects would occur.

Detoxification mechanisms that have been proposed for metals
include binding to metallothioneins (MT), which are proteins
having a high affinity for some metals. This mechanism appears
to be ubiquitous among organisms; these proteins have been de¬
scribed in organisms throughout the animal kingdom (Kagi and
Nordberg, 1979). They were first characterized in mammals and
now have been found to have a similar function in fishes, inver¬
tebrates, and plants. MT represent a family of inducible, low-
molecular- weight (LMW) , intracellular, cytoplasmic proteins that
normally bind seven to ten atoms of metals per molecule. These
proteins have been isolated from kidneys and livers of both
vertebrates and invertebrates. MT possess a number of unique
structural and functional characteristics. They contain 2 5 to
35 percent cysteninyl residues and lack histidinyl and aromatic
amino acid residues. All cysteinyl-SH groups are involved in
complexation of metal ions and do not form either intra- or
intermolecular disulfide bonds. The mode of distribution of
cysteinyl residues within the amino acid sequence is highly
conserved among isoforms of the protein from the same organisms,
as well as those isolated from taxonomically distinct organ¬
isms. Recently, considerable information has become available
on the mode of action and genetic control of MT.

The induction of the synthesis of MT has been demonstrated
in aquatic animals exposed to metals. The induction of MT is a
very significant process, not only because it appears to be im¬
portant in detoxification, but also because it can confer in¬
creased tolerance to organisms. For some species, this toler¬
ance results in increased survival of aquatic organisms and
their communications; this phenomenon is of significance to
those managing aquatic resources.

On the west coast, research on MT in fishes and inverte¬
brates has been performed by Dr. Kenneth Jenkins and coworkers
at California State University at Long Beach (Jenkins et. al.
1984), Dr. David Brown and coworkers at SCHWRPP (Brown et^ al.
1984), Dr. Guri Roesijadi and coworkers at Pacific Northwest
Laboratory at Sequim (Roesijadi et. al. 1982, and by our group
at Lawrence Livermore National Laboratory (Harrison et al. 1983).

110

Our investigations of metal metabolism in mussels involved
studies of both laboratory and field populations. Standard
biochemical methods were used to separate metal-binding
proteins. The mussel tissue that was used was the digestive
gland, which is known to concentrate metals and is homologous to
the liver of mammals. Digestive glands from 25 mussels were
pooled, homogenized, centrifuged at 100,000 x g, and then an
aliquot of the supernatant fluid was applied to a gel permeation
chromatography column. The column effluent was monitored for
absorbance in the UV region and collected in a fraction
collector. Sample fractions were analyzed for each metal. Two
metal peaks are generally found. The first peak represents
metals associated with high-molecular- weight (HMW) proteins and
the second peak with low-molecular-weight (LMW) proteins. The
HMW proteins include metalloenzymes that are necessary for
normal metabolic activities and are considered to be the sites
of toxic action of metals; the LMW proteins include metallothio-
neins that are considered to be the sites of detoxification.

The changes in the amounts of copper associated with these
two sizes of proteins are shown for digestive glands of mussels
that had been exposed for three weeks to 25, 50, and 75 pg Cu/L
(Figure 2). The quantities of copper associated with both the
LMW and HMW proteins were greater in those exposed to copper.
However, whereas the amount in the HMW proteins increased with
exposure concentration, that associated with the LMW proteins
was highest in those that had been exposed to 50 ug Cu/L. These
results indicate that exposure to 75 pg Cu/L for three weeks was
not well tolerated. This was indicated also from the mortality
data that showed a large percentage of mortality in the group
exposed to 75 pg Cu/L. Although the mortality was correlated
with the amount of Cu associated with the HMW peak (Figure 3),
it does not establish a cause-effect relationship.

A second experiment in which mussels were exposed to 25 ug
Cu/L for 12 weeks was performed. The quantities of metals as¬
sociated with the HMW and LMW proteins was quantified; the a-
mount associated with the HMW proteins continued to increase
with time whereas that associated with the LMW proteins MT ap¬
peared to plateau (Figure 4). The presence of a plateau indi¬
cates that the quantities of MT that are produced are limited,
which, in turn, implies that the detoxification provided by this
process is also limited.

It has been established that pre-exposure to low concen¬
trations of metals may result in the induction in the synthesis
of MT; this phenomenon may account for the large increase be¬
tween 3- and 6-week samples in the amount of copper associated
with LMW proteins. It has also been established that increased
concentrations of MT results in increased tolerance to exposure
to additional metals. In our experiments, the possibility of
increased tolerance to copper was not examined.

Ill

Copper (1x10* /nmoles/g wet weight)

Figure 2. Copper profiles constructed from gel permeation
chromatography from 100,000 x g supernatant fluid of homogenized
digestive glands from 25 mussels. HMW designates high-molecular-
weight protein fraction containing metalloenzymes ; LMW designates
low-molecular-weight protein fraction containing metallothionein.
The numbers adjacent to the curves indicated the concentrations
of copper to which the mussels were exposed.

112

- 37.5

x

a

CL

O

o

200 -

5 150 -

o

E

a

100 -

- 12.5

25 50

Copper (jug L'1)

Figure 3. Percent mortality after 21-day exposure to copper
compared to the concentration of copper in the high-molecular-
weight protein fraction.

113

Mortality (%)

Copper (1x10 /xmoles/g wet weight)

Figure 4. Changes in the quantities of copper in the high
molecular-weight (HMW) and low-molecular-weight. (LMW) Protein
fractions in the supernatant fluid from homogenized digesti
glands from 25 mussels that had been exposed to 25 pq Cu/t

114

A third experiment was performed to determined the effect of
exposure to copper for longer periods of time than were used in
the first two experiments. Mussels wee exposed to 10 and 25 ug
Cu/L for 21 weeks. In those that were exposed to 25 ug Cu/L,
there were large increases in the quantities of copper associ¬
ated with both the HMW and LMW proteins, whereas in those
exposed to 10 ug Cu/L, there were large increases only in the
LMW proteins (Figure 5). These results indicate that detoxifi¬
cation provided by the MT found in the LMW protein was adequate
to prevent built-up of copper in the HMW protein fraction that
contains enzymes critical for normal metabolism.

In field studies we investigated the kinds and quantities of
metals associated with these same proteins in populations from a
pristine environment (Tomales Bay, CA) and in those from a con¬
taminated environment (South San Francisco Bay). In addition,
we participated in a mussel-transplant study with Dr. John
Martin (California Department of Fish and Game); bagged mussels
from Tomales Bay were distributed in an array near a municipal
outfall in the Southern California Bight and sampled sequential¬
ly with time.

Field populations of mussels from the two sites were found
to differ in the distribution of metals between the LMW and HMW
metalloproteins (Table 1). It is apparent that the South San
Francisco Bay mussel were contaminated highly with copper and
cadmium. In mussels transplanted from Tomales Bay to the White
Point outfall in the Southern California Bight, the concentra¬
tions of metals associated with the LMW and HMW proteins in¬
creased significantly after 1- and 3-month exposure to the
effluent (Table 2). Copper, cadmium, and zinc were rapidly
accumulated in the LMW protein fraction containing the MT, and
some displacement of the essential metal, Zn, may have occurred.
However, interpretation of the results was confounded because no
measurements of the levels of MT were made. We currently have a
methodology for quantifying MT, and in our future transplanta¬
tion studies, we will follow both the concentration of MT and
the metals associated with both LMW and HMW metalloproteins.
Results from these kinds of experiments will provide a better
understanding of metal metabolism and adaptive capabilities of
mussels from pristine and metal-contaminated ecosystems.

Organic Compound Metabolism

Marine bivalve molluscs efficiently concentrate organic
chemicals present in the water. Whether an organism will be
harmed by accumulated contaminants is determined largely by its
ability to transform them into more water-soluble (detoxified)
forms. Some metabolic transformations, however, result in the
production of activated compounds that are more toxic than the
original contaminants.

115

Figure 5. Changes in the quantitites of copper in the high-
molecular-weight (HMW) and low-molecular-weight (LMW) protein
fractions in the supernatant fluid from homogenized digestive
glands from 25 mussels that had been exposed to either 10 or
25 jig Cu/L.

116

Table 1. Concentrations of metals in the high-molecular-weight
(HMW) and low low-molecular-weight (LMW) (1 x 10”4 umoles /g
wet weight) protein fractions in the supernatant fluid from
homogenized digestive glands from 25 mussels from Tomales Bay
and South San Francisco Bay.

TOMALES

BAY

SOUTH SAN

FRANCISCO BAY

HMW

LMW

HMW

LMW

Zinc

330

770

460

1320

Copper

10

330

480

3600

Cadimum

ne£

ND

140

1600

Total

340

1100

1080

6520

a ND, none detected

117

Table 2. Concentrations of metals in the high-molecular-weight
(HMW) and low low-molecular-weight (LMW) (1 x 10 4 umoles /g
wet weight) protein fractions in the supernatant fluid from
homogenized digestive glands from mussels that were transplanted
to the White Point outfall in the Southern California Bight.

The first sampling was taken after one month and the second
after three months. Each sampling included 25 mussels.

SOUTHERN CALIFORNIA BIGHT

SAMPLE 1 SAMPLE 2

HMW

LMW

HMW

LMW

Zinc

1600

2000

700

1600

Copper

400

1700

550

3500

Cadmium

80

130

430

540

Total

2080

3830

1680

5640

118

Our studies are concerned particularly with energy-related
organic contaminants that are potentially mutagenic or carcino¬
genic. Many such compounds are present in the water-soluble
fraction of fuel oils and are rapidly accumulated by aquatic
organisms.

Aromatic amines represent a class of organic contaminants
that are present in a variety of industrial and energy-related
wastes. The biological hazard posed by these compounds is
largely determined by their biotransformation; that is a
specific metabolic reaction (N-hydroxylation) is required before
they elicit mutagenic or carcinogenic effects. Unfortunately,
little is known about the ability of aquatic organisms to
metabolize these contaminants. In our studies we have developed
experimental protocols that can be used to assess the in vivo
metabolic processing of these and other organic contaminants by
marine invertebrates. Such basic information is needed because
our knowledge of chemical metabolism has been based largely on
studies of vertebrate organisms and may not directly apply to
invertebrate species. With increased understanding of biotrans¬
formation in marine mussels, we will be better able to predict
the effects of organic contaminants found in contaminated
ecosystems.

For our experiments we chose to study the metabolic trans¬
formation of a model aromatic amine (o-toluidine) whose struc¬
ture is representative of a broad class of potentially mutagenic
contaminants. The mussels that we used in our initial experi¬
ments were from Tomales Bay. These mussels rapidly accumulated
o-toluidine and eliminated metabolites that were significantly
different from those produced by vertebrate organisms (Figure
1) . Mussels and vertebrate organisms form different metabolites
because they have different detoxification mechanisms. In addi¬
tion to producing mutagenically activated (nitrogen-oxidized)
metabolities, the mussels were able to add a single carbon atom
to the nitrogen atom and form a novel detoxification product,
n-formyl-o-toluidine. This nitrogen metabolizing pathway repre¬
sents a significant departure from the two-carbon addition (ace¬
tylation) that is usually observed in vertebrate of this common
detoxification pathway. The common carbon-oxidizing metabolic
pathways that we expect to occur in mammals were not found in
the mussels? we did verify our experimental techniques by
isolating these metabolites from a rat injected with o-toluidine
(Figure 6).

The pathways available to mussels for the metabolism of
aromatic amines consist of reactions that the organisms normally
utilize for the metabolism of amino acids, fatty acids, and
proteins. Any change in the organism's ability to metabolize a
foreign compound (i.e., o-toluidine) should therefore be
indicative of its overall physiological state. We investigated
this hypothesis by measuring the metabolic capabilities of

119

MOLLUSCS

N = 0

/

Figure 6. The biotransformation of a model aromatic amine
(o-toluidine) by a marine mollusc (bay mussel) , marine flat¬
fish (starry flounder) , and Sprague-Dawley rat. The nitrogen-
oxidizing capability of mussels is significant in as much as
all mutagenic and carcinogenic aromatic amines require metabolic
activation via this pathway. That is, the aromatic amines
themselves are not harmful but their nitrogen-oxidized metabolites
are capable of causing damage to biomolecules.

120

mussels taken from a site of known contamination in San
Francisco Bay. Mussels were collected from a site at Redwood
City where the California Department of Fish and Game has
documented their bioconcentration of metals, synthetic organic
chemicals, and petroleum hydrocarbons (Stephenson et. al.

1982). In our comparative study (Table 3) we found that the
total extent of o-toluidine metabolism in mussels from South San
Francisco Bay was significantly less than mussels from Tomales
Bay (Knezovich and Crosby, 1985). These results are in agree¬
ment with the findings of Martin et. al. (1984) who reported a
diminished physiological condition, as evidenced by a reduced
scope for growth, in mussels taken from this site.

We are currently using our understanding of aromatic amine
metabolism to better understand the effects of contaminant-
induced stress. Mussels transplanted from Tomales Bay are being
monitored for changes in their abilities to metabolize both
metallic and organic contaminants. The results of this study
will help us to define limits of physiological adaptation so
that realistic evaluations of impacted populations can be made.

Acknowledgements

This work is supported by the Ecological Research Division
of the U.S . Department of Energy; Office of Health and Environ¬
mental Research. Work is performed under the auspices of the
U.S. Department of Energy by Lawrence Livermore National Lab¬
oratory under Contract W-7405-Eng-48.

References

Bayne, B.L., ed., 1976: Marine Mussels: Their Ecology and
Physiology. Cambridge University Press, London.

Brown, D.A.; S.M. Bay; J.F. Alfafara; G.P. Hershelman; and K.D.
Rosenthal, 1984: Detoxification/toxification of cadmium in
scorpionfish fScoroaenaguttata) : acute exposure. Aguatic
Toxicol. 5:93-107.

Goldberg, E.D.; V.T. Bowen, J.W.; Farrington, G. Harvey; J.H.
Martin; P.L. Parker; R.W. Risenbrough; W. Robertson; E.
Schneider; and E. Gamble, 1978: The mussel watch. Environ.
Conserv. 5:1-25.

Harrington, F.L.; J.R. Lam; and R. Berger, 1983: Sublethal

responses of Mvtilus edulis to increased dissolved copper.
The Science of the Total Environment. 28:141-158.

Hatch, T, 1962: Changing objectives in occupational health. Am.
Ind. Hyg. Assoc. 23:1-7.

121

Table 3. The comparative metabolism of o-toluidine by Mytilus edulis
from pristine (Tomales Bay) and contaminated ecosystems (San Francisco
Bay ) .

Metabolites produced

l in 8 hr.

(pmole/mg dry wt . )

Metabolites

Tomales

San Francisco

N -Hydroxy -o-toluidine

2.4(0. 1)

NB

2-Nitrosotoluene

22.2(14.2)

9 . 5 ( 2 . 7 )

N -Methyl -o-toluidine

29.3(16.0)

9 . 3 ( 3 . 9 )

N -Formyl -o-toluidine

27.9(13.8)

9 . 7 ( 1 . 6 )

Sum of pathways

81.8(44.2)

28.5(6.6)

ND, none detected

Standard deviation in parentheses.

122

Jenkins, K.D.; B.M. Sanders; and W.G. Sunda, 1983: Metal regu¬
lation and toxicity in aquatic organisms. In T. Singer, T.
Mansour and R. Ondarza, eds., Mechanisms of Drug Action.
Academic Press, New York, p. 277.

Kagi, J.H.R. and M. Nordberg, 1979: Metallothionein:

Proceedings of the First International Meeting on Metallo-

thionein and Other Low-Molecular-Weight Binding Proteins.

Birkhauser Verlag, Boston, pp. 378.

Knezovich, J.P. and D.G. Crosby, 1985: Fate and metabolism of;
o-toluidine in the marine molluscs Mvtilus edulis and
Crassostrea gigas. Environ. Tox. Chem. 4:435-446.

Martin, M., G.; Ichikawa, J.; Goetzl, M. De Reyes; and M.D.

Stephenson, 1984: Relationship between physiological and
trace toxic substances in the bay mussel, Mvtilus edulis.
from San Francisco Bay, California. Mar. Environ. Res. 11:
91-110.

Roesijadi, G.; A.S. Drum; J.M. Thomas; and G.W. Fellingham,

1982: Enhanced mercury tolerance in marine mussels and

relationship to low-molecular-weight, mercury-binding
proteins. Mar. Pollut. Bull. 13:250-253.

Stephenson, M.D.; S.L. Coale; M. Martin; D. Smith; E. Armbrust;

E. Faurot; B. Allen; L. Cutter; G. Ichikawa; J. Goetzl; and
J.H. Martin, 1982: California state mussel watch 1980-81.
Trace metals and synthetic organic compounds in mussels from
California's coast, bays and estuaries. State Water Re¬
sources Control Board, Water Quality Monitoring Report 81-11
TS. Sacramento, CA, pp. 1-72.

White, K.M., 1937: Mvtilus. Mem. Liverpool Mar. Biol. Comm. 31.

123

SCIENTIFIC INFORMATION AND MANAGEMENT POLICY

FOR THE DELTA-SAN FRANCISCO BAY ECOSYSTEM

Michael J. Herz and Michael A. Rozengurt
Paul F. Romberg Tiburon Center for Environmental Studies
San Francisco State University

Abstract

Despite the many attempts to create a useable data base with
which to develop management policies for the Delta- Bay ecosys¬
tem, there is currently no agreement among scientists, resource
managers, dischargers, and the public on a decision-making
process that will lead to effective management. This paper
proposes a procedure for developing management goals, scientific
questions, research programs, conclusions, and recommendations
leading to solutions for major estuarine problems based upon the
systems analysis approach. The approach is illustrated with a
number of systems block diagram examples.

Thus far in this seminar presentation, there has been much
discussion about science but little direct mention of management
of the resources of San Francisco Bay and the Delta. However,
it is important to realize that these earlier presentations have
been about resource management because the data that have been
presented -- the actual parts per million of pollutants in
striped bass and the number of million acre feet of freshwater
flowing into San Francisoc Bay from the Delta and rivers (after
diverisons) — are all by-products of management decisions.

They are measurements of the effectiveness of the management
process.

In fact, most of us believe that the status of the Delta and
Bay and their natural resources has been determined to a great
extent by prior management decisions. The problem is that we
can't prove it. If we could show that the decline in freshwater
inflow to the Delta and Bay or level of pollutants in the water
caused the radical decline in striped bass, it would be
relatively easy to convince resource managers that policies must
be changed. The best that we can do is to find significant
correlations (associations) between several of those factors
(e.g., Rozengurt, Josselyn and Herz, this volume). Convincing
resource managers that the findings the sufficient to warrant
policy changes requires our developing the most powerful
analytical techniques and the best scientific information and
communicating it as clearly and concisely as possible in order
to assist them with their decision-making.

125

When one works in the arena of policy and management
decision-making, it becomes evident very quickly that scientists
and managers view the world, and each other, quite differently.
Managers often see scientists as intent on collecting unlimited
quantities of irrelevant data over infinite time periods, and as
not wanting to state conclusions without significant qualifying
language. Perhaps it is this quality that once led Senator
Proxmire to lament that he wanted more one-armed scientists,
ones who would not say, "But on the other hand . "

On the other hand, scientists view managers (and politi¬
cians) as not understanding the need for large data bases col¬
lected under standardized conditions over long periods of time
before conclusions can be reached with any degree of certainty.
They judge the manager's quick decisions, based on what they
consider insufficient information to be arrogant guesses, or
worse, purse political expediency.

The purpose of this paper is to show that each set of
players needs to learn from the other, and that there do exist
procedures for maximizing the degree to which decision-making,
policy development and resource management can utilize technical
information.

This combination of circumstances surrounding the status of
ecological information on the River- Delta- Bay-Ocean ecosystem
indicates that we have serious problems regarding the adequacy
of information on the resources that we are trying to manage.

It also indicates that there does not exist an agreed-upon set
of management goals for this, the largest estuary on the Pacific
coast. Despite the over $3 billion spent on improving Bay water
quality since the passage of the Clean Water Act in 1972, and
despite the presence of over 75 agencies, academic institutions,
and non-profit organizations concerned with the Bay and environ¬
mental issues, we have yet to develop a system which established
widely accepted management goals. One Bay scientist expressed
his concern over this problem as follows (Conomos, 1977):

In response to environmental concerns during the past few
decades, legislative committee have agreed that this estu¬
arine system should be protected against further indiscrim¬
inate and unrestrained exploitation. These committees and
subsequent Federal and state legislation have mandated that
sound plans for long-term intelligent and rational manage¬
ment of this valuable resource be formulated and imple¬
mented. There is, unfortunately, little scientific data on
which to base these plans. Our knowledge of the complex
physical, chemical, biological, and sedimentological estu¬
arine processes is relatively primitive. This is surpris¬
ing, considering the importance and irreplaceable nature of
the system, the magnitude and cost of the public works al¬
ready built or in the planning stages, and the demands and
standards imposed by environmental and regulatory agencies.

126

On the other hand, there is the view expressed by an in¬
dustry managers that although you don't have all of the informa¬
tion that you need to make the best management decisions, you
must

. -9° ahead and start making some wild guesses based on

the information you have. Make your best possible esti¬
mates, because if you don't make those estimates, the mana¬
gers and the decision-makers are going to ignore you and go
ahead and decide anyway, in the absence of any data (Adams,
1982).

So the question becomes, how do we chart a course through
these troubled waters to find agreement? From the perspective
to those concerned with the role of scientific information in
the decision-making and management processes, we should begin by
developing a set of management goals which are agreed to by
managers, scientists, politicians, and the public. From this
set of goals, it should then be possible to devise scientific
questions which become the basis for a research program designed
to produce information and recommendations that support the
management goals or lead to their modification to better meet
the environmental needs of this estuarine ecosystem. Schemati¬
cally, the approach is as follows:

RECOMMENDATIONS < - r

i

MANAGEMENT GOALS

1

SCIENTIFIC QUESTIONS

i

RESEARCH PROGRAM DESIGN

i

DATA

i

CONCLUSIONS - ‘

From the earlier discussion, it is obvious that neither the
development of the management goals nor the design of the
research program should become the exclusive domain of either
scientists or managers. Rather, a Management Policy Committee
should be created which has representation from both groups as
well as from relevant industries and the public. Since research
design requires specialized technical knowledge, a Technical
Advisory Committee should be formed which consists of a multidis¬
ciplinary set of scientists from management agencies (Federal,
state, and regional), research institutions, industry, and
public oragnizations. Both of these committees should have
representation from each of the categories of Bay Area interest
groups:

127

San Francisco Bay Interest Groups

Regulatory Agencies

Environmental Protection Agency
U.S. Army Corps of Engineers
Bureau of Reclamation
U.S. Fish & Wildlife Service
CA Dept, of Water Resources
CA Dept, of Fish and Game
Studies

State Water Resources Control
Board

Regional Water Quality Control
Bds. (S.F. Bay and Central
Regions)

Bay Conservation & Development
Commission

Non-Profit Organizations

Committee for Water Policy
Consensus

Citizens for a Better Environ¬
ment

Environmental Defense Fund Bay
Institute
Oceanic Society
Save San Francisco Assn.

Bay Wetlands Coalition

Audubon Society

Natural Resources Defense Fund

Research Organizations

Uni. of California Berkeley
Sanitary Engineering Research
Lab

Lawrence Livermore Laboratory
San Francisco State Univ.
Tiburon Ctr. for Envir.

U.S. Geological Survey
National Oceanic and Atmos¬
pheric Administration
Aguatic Habitat Institute

Dischargers

Bay Area Dischargers Assn.

Bay Area League of Industrial
Associations

While the management structure is important, the future of
the Delta and San Francisco Bay will be determined by whether or
not solutions are developed for its problems, many of which have
already been identified:

o Decreases in freshwater inflow have resulted in major

reductions in flushing activity (increases in renewal time)
and reductions in fish stocks to all-time lows (Rozengurt,
Josselyn, and Herz, this volume).

o Pollutant loads in some species of fish and wildlife are so
high that warnings have been issued to protect public
health; these loads may be responsible for reproductive
failure and population deterioration (Whipple, this volume).

o Pollutant discharges from industrial and municipal dis¬
chargers, agricultural, and non-profit sources are in¬
creasing (Nichols, et at. 1986).

128

o Reduction in wetland habitats has eliminated fish nursery

and waterfowl migration and nesting areas (Josselyn, this

volume) .

One technique for developing an appropriate research program
and management scheme for addressing these problems is the sys¬
tems analysis approach, which has been used successfully in the
space prgram. Its procedures are especially useful, since they
were designed to analyze the organization and interrelationships
among components of complex systems such as those found in nat¬
ural environments.

Figures 1 and 2 show schematically the processes of formu¬
lation and solution of estuarine problems. These, along with
decision-making, decision implementation, and analysis of differ¬
ences between the predicted results and those obtained, are the
major parts of system methodology for solving multiple prob¬
lems. The application of a programmatic approach to organi¬
zation of complex systems raises a variety of methodological
operations related to water resources management and research.

The first category of operations are those which relate to:

1) formulation of problems and objectives, i.e., de¬
scription of the current conditions or the results of
scientific investigations;

2) outlining "the tree of objectives";

3) developing a system of water resources management;

4) creating an operational model of system's functions;

5) establishing a research program designed to achieve the
desired objectives; and

6) implementing the research program.

Formulation of the problem is particularly important in a
programmatic approach since it determines the development of
subsequent investigations. The most appropriate methodology for
problem identification is based upon the system analysis ap¬
proach. According to this methodology, the process of problem
formulation represents a chain of consecutive analytical and
synthetic operations (Figure 3):

1) evaluation and interpretation of the status of the
ecosystem including description of trends in various
parameters and their interactions. (Determine objec¬
tive) ;

2) identification of problems and undesirable trends;

129

Procedure for formulating Environmental Problems
of Estuarine Ecosystems
(San Franc’sco 8ay)

Figure 1. The scheme of the procedure for formulating environmental problems
of estuarine ecosystems. (1) flow of information; (2) order of operation and
flow of information

130

Problem Solving Procedure

Figure 2. The scheme of systems analysis approach related to solving
environmental problems of the Delta-San Francisco Bay Ecosystem.

131

f U9SYSTCM : KCONOLOQY

SC3N0KV A%0 £C0LX»;

III

IV

VI

Economic and ecolof’ca bases of wate
development and management

- * - - - 7^ -

■*eograpnic 4nd Env irorwwenta I LCOn^'c

ko^owic a rx3 economic evaluation

Structure 0f cnttrii of of priorities

the "'V«r Optimal function for water - — —

estuarine 0f estuarine deve I ooment

ecosystem system and management

f undart
economic basis
• at tr development
--•-schemes and water
constr vat i on
a 1 ternati ves

Economic evaluation of
•nv ironmenta 1 resources
of the ecosystem

" — • 1 1 f

Analysis of
hi stor ica 1
trends of water
development and
population
growth

.: i . .=:

Eva I uat ion of water
factor as a means
of re gu 1 a 1 1 on o f
populations and
industrial growth

Determination of critical
levels of economic
growth of major water
users and developers
if no conservation
alternatives are
implemented for conditions
of 3 - 7 years consecutive
drought

Principles of
economic
effect i venes s
of water
devt 1 ooment
related to
biological toler¬
ance of ecosystem
T

i

•

x

Probability limits
of demands for
water by different
— (^branches of
government
ith restricted
amounts of natural
r unof f

Integra 1
bioeconomic
charactenst ics
of dynamic
equ 1 1 ibr i urn
between water
users and water
developers in
Cal i forma

Other Unforeseen Probli

Cost effective-
ne ss a^alysu
of water use by
d i f f erent
conveyance
systems aod
their

ecologica I
impact on
the Delta

±

valuation of the
fficiency of
water utilisation
in various
industries
- 1 -

Analysis of the
economic indices
and incentives
related to waterf-
management in
d i f ferent
branches of
industry

Risk/Benefit
analysis for:

- agriculture

- industry

- muni c i pa 1 1 1 1 es

- fisheries

- recreation
T

State's emergency
water balance
forecast and its
economic criteria
in case of terror¬
istic poisoning of
major water supply
or of nuclear
i nc i dent

1

A1 ternative
recommend at i on

Figure 3. Hierarchy of investigations of the interrelations between ecological
and economic indices of development in California under various levels of water
supply for the Delta-San Francisco Bay Ecosystem.

132

3)

development of alternative solutions and techniques for
modification of negative trends. (Techniques for
meeting objectives);

4) assessment of impacts of alternative solutions (Compare
with objectives);

5) identification of "best" alternative based on optimal
use of environmental resources balanced with needs of
the economy.

The process starts with investigations of all water re¬
sources of the region, their dynamics (under natural and regu¬
lated conditions), quality and biological productivity, as well
as their uses, conservation, and restoration. This makes it
possible to describe the trends in various dimensions of the
ecosystem and to define optimal levels of resources utilization.

Then a long-term forecast begins with water availability
studies and analysis of water use by various industries, demo¬
graphic trends, and recreational needs in this particular re¬
gion. Based on a variety of projected levels of water use, fore¬
casts are then made of potential impacts of water regulation on
the quality of the estuarine ecosystem and its living resources
(e.g., fisheries, wildlife, etc.). The main objective of this
systems analysis approach is the development of a tentative eval¬
uation of long-term trends in water resources. This should then
make it possible to identify the principal factors responsible
for these changes and to develop strategies for their mitiga¬
tion. Decisions regarding alternative strategies will utimately
be made through a management system.

The Environmental Protection Agency (EPA) has recently
assumed a leadership role in this process to "achieve effective
and cooperative management of the Delta- Bay system and to facili¬
tate communication and coordination among and within existing
management agencies." Their initial step will be to design a
management structure and decision-making process. In order to
manage the Delta and San Francisco Bay for the benefit of all
the citizens of the area, management goals that are agreed upon
by a wide and representative cross-section must be adopted and a
research program designed to achieve these goals.

A likely source of information needed for such management is
the recently created Aquatic Habitat Institute (AHI) which is
governed by a board representing regulatory agencies, discharg¬
ers, the academic community and the public, and which was de¬
signed to produce a "a comprehensive data base for current and
past research, and master plan for future monitoring and re¬
search that assures efficient use of the many ongoing pro¬
grams." It is anticipated that the AHI will work closely with

133

the EPA to address many of the first year priorities agreed upon
at EPA's recent San Francisco Bay/Delta Estuarine Management
Project meeting: identify, locate, coordinate, and disseminate
existing information on the estuary; identify additional data
needs; develop quality assurance and quality control measures;
initiate long-term monitoring; and develop public participation
and education programs focused on policy goals.

Scientist, managers, dischargers, and the public must reach
consensus on this management plan and on the scientific
questions that need to be answered before the program is
undertaken. From our perspective, it is clear that the systems
approach described here can play an important role in organizing
and understanding this highly complex estuarine system. We are
hopeful that the EPA and AHI will use it as part of the planning
and management process.

Acknowledgements

This research was supported by grants from the San Francisco
Foundation/ Buck Trust. The authors gratefully acknowledge the
technical assistance of Douglas Spicher.

References

Adams, J., 1982: Discussion of " Bioeconomic models and the

development of a San Francisco Bay fisheries index." In M.
Herz and S.M. Creary, eds., 1982 State of the Bay Conference
Proceedings. The Oceanic Society, San Francisco Chapter, p.
181.

Conomos, T., 1977: Introduction. In T. Conomos, ed., San

Francisco Bay: The Urbanized Estuary. Pacific Div. Amer.
Assoc, for the Advancement of Science. San Francisco, p. 7.

Nichols, F.H., 1987: Benthic ecology and heavy metal accumu¬
lation. In San Francisco Bay: Issues. Resources. Status,
and Management. NOAA Estuary-of-the-Month Seminar Series
No. 6. Washington, D.C., U.S. Department of Commerce, NOAA
Estuarine Programs Office, p. 65-67.

Nichols, F.H.; J.E. Cloern; S.N. Luoma; and D.H. Peterson, 1986:

The modification of an estuary. Science. 231:567-573.

Rozengurt, M.A.; M.J. Herz; and M. Josselyn, 1987: Impact of

water diversions on the river-bay-estuary-sea ecosystems of
San Francisco Bay and the Sea of Azov. In San Francisco
Bay: Issues. Resources. Status, and Management. NOAA

Estuary-of-the-Month Seminar Series No. 6. Washington, D.C.,
U.S. Department of Commerce, NOAA Estuarine Programs Office,
p. 35-62

134

Whipple, J.A.; R.B. MacFarlane; M.B. Eldridge; and P. Senville,
Jr., The impact of estuarine degradation and chronic pol¬
lution on populations of anadromous striped bass in the San
Francisco Bay- Delta: A summary. In San Francisco Bay:
Issues. Resources. Status, and Management. NOAA Estuary-
ofthe-Month Seminar Series No. 6. Washington, D.C., U.S.
Department of Commerce, NOAA Estuarine Programs Office,
p. 77-107

135

SHORELINE MANAGEMENT

Alan R. Pendleton

Bay Conservation and Development Commission

I should first point out that other speakers have covered in
one form or another the scientific points about San Francisco
Bay that I wanted to make. But, because I am more familiar with
coastal management issues than problems faced by scientists, and
to avoid repetition, I will focus on how San Francisco Bay is
managed. Then I'd like to discuss two recent matters: mitiga¬
tion policy and diked historic baylands to help show how science
does or does not interact well with the coastal manager's needs.

I would like to give you a little more information about the
Commission's organization and jurisdiction. The Commission is a
state agency, but one with only regional jurisdiction over San
Francisco Bay. There are 27 commissioners. The 13 local re¬
presentatives dominate the Commission's decisions. These
locally appointed commissioners are from the 25 cities and 9
counties that control territory in or along the Bay. There are
five state commissioners including representatives from the
Regional Water Quality Control Board, tbe State Lands Commis¬
sion, the State Resource Agency, the State Department of Trans¬
portation, and the State Department of Finance. There are five
commissioners appointed by the Governor, including the Chairman
and Vice-Chairman. One commissioner is appointed by the Speaker
of the Assembly and one by the State Senate. There are also two
Federal representatives: the District Engineer from the San
Francisco District of the U.S. Corps of Engineers and the Region¬
al Administrator for Region 9 of the Environmental Protection
Agency. It takes 13 affirmative votes to grant a permit and 18
affirmative votes to adopt or change a policy in the San
Francisco Bay Plan.

The McAteer-Petris Act defines the Commission's jurisdiction
and authority. The jurisdiction includes all areas of the Bay
from a line westerly of the Golden Gate to a line at the Delta
that is subject to tidal action, including marshes, salt-ponds,
managed wetlands and portions of certain tributaries that flow
into the Bay. There is also jurisdiction over the shoreline for
the first 100 feet inland from the edge of the Bay. Within this
area, permits from the Commission are needed for any filling,
extraction of materials, and substantial changes in use. The
Commission also has planning responsibilities for the Bay as a
regional resource of statewide significance.

137

The Act was the first comprehensive coastal management law
in the country. In the 2 0 years it has been in effect, it has
worked remarkably well. This law instructs the Commission to
balance the need to preserve the natural values of San Francisco
Bay with the need to accommodate economic uses of the Bay.
However, if there is an unavoidable conflict between those
goals, preservation of the Bay predominates.

The San Francisco Bay Plan establishes the policies that
govern the Bay. The 1965 version of the Act charges the
Commission with preparing a comprehensive plan for the Bay in
three years. The resulting planning program involved consider¬
able research summarized in many technical reports. Some titles
of these reports may give you some sense of the range of the
investigation.

(1) Geology of the Bay;

(2) Mineral Resources of the Bay;

(3) Sedimentation Aspects of the Bay;

(4) Effect of the Bay on Climate;

(5) Ecological Aspects of the Bay;

(6) Tides of the Bay;

(7) Water Pollution and the Bay;

(8) Regional Organization for Bay Conservation and
Development;

(9) Municipal, State and Federal Programs Affecting the
Bay; and

(10) Air Transportation of the Bay.

This is only a sample -- a number of other reports dealt
with ownership, regulatory authority, recreation, public facili¬
ties, barrier proposals, safety of fills, surface transporta¬
tion, waterfront housing, waterfront industry, taxation, fund¬
ing, and similar matters that affect how the Bay is governed.

Thus, both the McAteer-Petris Act and the Bay Plan address
the Bay's resources from a number of points of view. Certainly
preserving the Bay is the foremost priority in both the law and
the Plan. Because there were several areas where information
was lacking and because priorities and values change over time,
the Legislature instructed the Commission to make a continuing
review of all aspects of the Bay. Since 1969, the Bay Plan has
been revised to reflect new information and to adopt new or
changed policies. The most important planning efforts since
1970 include the studies that led to the Suisun Marsh Protection
Plan, the study on dredging in the Bay, the studies that led to
the Richardson Bay Special Area Plan, the diked historic bay-
lands study, and the Seaport Plan. In addition to a well
written law and a comprehensive plan for the Bay, the Bay also
enjoys strong judicial and public support.

138

California is fortunate in having legal precedents that
support broad regulatory authority -- certainly broader than
exist in many other states. The California Supreme Court
generally allows government to wield considerable police
authority when making land-use decisions. That allows the
Commission to be a little more aggressive than other commissions
can be when faced with a choice between man's activities in the
Bay and the need to preserve the natural values of the Bay.

The "public trust" doctrine also supports better decisions
for the Bay. The public trust is a type of public property
interest in the tidelands and submerged lands of the Bay. It is
held by the state on behalf of the people and is paramount to
any private property interests that may also exist. It can be
thought of as an easement. The Commission is one of the co¬
trustees of this public trust. The McAteer-Petris Act is a
declaration of the Legislature concerning what the public trust
more specifically means for the Bay. When the Commission is
acting in its capacity as a co-trustee, it can restrict uses on
private lands more completely than it could if it were only
using police power. If you use the police power in a way that
deprives an owner of his property rights without paying for
them, you are subject to a lawsuit that may require the agency
to pay for the land affected by the decision. This possibility
obviously has a chilling effect on the willingness of govern¬
ment to approach the line of an overly restrictive land-use
decision. But if you are applying public trust principles to
the land, then you are acting as one of the owners. An owner
usually has greater control over property than a regulatory
agency.

Public opinion supports an unfilled Bay. There is a fairly
broad consensus among the citizens of the Bay Area that the Bay
is important, valuable, and deserving of protection. Most Bay
Area "leaders" recognize that the Bay Area is at a competitive
disadvantage in comparison to most other regions. For example,
our ports are disadvantaged in comparison with the deeper
watered and richer Ports of Los Angeles, Long Beach, or Seattle.
Housing costs in the Bay Area are among the highest in the
country -- that discourages new industry. Chip-based technology
has been experiencing retrenchment recently due to foreign
competition and a maturing marketplace. Education and other
public services have been contracting in the wake of Proposition
13, which greatly limits public taxing of property. Transpor¬
tation is expensive, and roads are jammed and often badly
maintained. Sewers need replacement in many areas.

139

Against these many competitive disadvantages, the Bay
provides a great amenity and resource. It defines the area as
special; the water creates vast open space and provides spectac¬
ular views. It moderates the climate. It is a great sailing
Bay. It is a nursery ground for fish. It contains the largest
contiguous marsh in California, a stopover for many mitigrating
waterfowl. This resource and the region's other environmental
advantages are our most important economic asset as well as
vital to our continued health and welfare.

Our social and political structure makes it more difficult
to govern the Bay as a single, interrelated entity. California
divides resource management by subject matter. There is no
department of environment or of natural resources. One agency
regulates air emissions; another controls discharges into the
Bay; a third decides who may take what freshwater where; a
fourth regulates fisheries; a fifth administers the state park
land-use; and a sixth, the Commission, plans for and regulates
land-use in and along the Bay. Add to this 25 cities with
councils, administrators, zoning and planning authority and 9
counties with supervisors, administrators, zoning and planning
authority. So, special effort must be made in the Bay Area to
cooperate to assure balance among the various agencies assigned
to protect natural values.

Through the 1966-1970 planning period, science always played
an essential role in defining the resources and describing the
natural processes. Science has played less of a role recently,
particularly in the regulatory decisions of the Commission.

This is because scientific information about the Bay is not or¬
ganized comprehensively, because research on the Bay has not
kept up with efforts made for other important estuaries, because
some scientific information is readily available in a form that
is useful to policy-makers and because some essential data about
the Bay has not been gathered. I believe that during the last
10 years or so, science has played less of a role in the de¬
cisions about the Bay than law, public opinion, politics, and
economics.

Lack of comprehensive information, lack of coordination
among various scientists and organizations doing research on the
Bay and, failure to provide existing information in a form that
is useful to managers are the likely reasons science has played
a smaller role than it should when decisions about the Bay are
made by the Commission, and I suspect, by other managers of the
Bay's resources.

Of course, commissioners vary in their reaction to a situa¬
tion in which there may be a threat to the natural values but
scientists are unable or unwilling to define the extent of the
threat clearly. In that situation, some commissioners will
ignore unquantified and unspecific threats. That often means

140

that an application is approved or less stringent policy lan¬
guage is adopted. An applicant usually has factual support for
this application and is willing to spend the money and effort it
takes to produce the scientific information needed. The scien¬
tific community is often in that position. Unless scientists
can provide reasonable assurance that a specific harm will
result unless a restrictive policy is adopted, the Commission
may prefer to err on the side of those affected by the
restriction.

Recently and frequently for matters before the Commission,
scientists have said there is little data relevant to the
question before the Commission. Or they state that the data
that is available has been brought into question and may not
provide a reliable basis for a decision. Or they say that the
only scientific opinion available has been extrapolated from
other areas which may or may not relate well to the Bay. But
commissioners must nevertheless decide. If scientists say they
cannot help much and decisions must be made, the Commission is
forced to deal with less than a full deck.

As Mike Josselyn has pointed out, coastal managers must have
easy access to scientific information. For San Francisco Bay,
there is a large number of academic and scientific institutions
that do various types of research on various aspects of the Bay.
It is not always easy to discover who has what information. We
need a clearinghouse or scientific forum that can coordinate the
various studies, share information among scientists, and inform
managers and the public about research, available data, and new
conclusions about the Bay.

As important as providing a clearinghouse, we need scienti¬
fic information written for the non-scientist. The non-scien¬
tists must be able to understand what the information means and
must be able to know why the information is important. If the
information is presented in a way that is too difficult for the
layman to understand, it is unlikely that decision-makers or the
public will either appreciate the importance of the research or
apply it to the decisions they must make.

Now, I'd like to talk about two specific areas of concern
the Commission has been working on where science has played an
important part. First, mitigation. Mitigation means many
things to different people. For the Commission, mitigation
means the addition to or restoration of an area to wetland
value. It does not mean buying out of harm that a project could
avoid. Nor does it mean that projects that otherwise do not
meet the requirements of our policies can be approved if mitiga¬
tion is provided. A project must first meet the requirements of
our law and Plan; it must be designed to have the least possible
adverse will, nevertheless, have adverse impacts on natural

141

values of the Bay. Then we require mitigation to offset those
unavoidable impacts. Federal agencies often refer to this type
of mitigation as compensation.

Now determining the adverse impacts of a small amount of
fill in the Bay, particularly if marshes and mudflats are not
involved, is very difficult. It is probably impossible to
quantify precisely such impacts. However, we can reasonably
assume that the cumulative impacts of several small fills, will
at some point, affect the natural values of the Bay, even though
it is difficult to assess the impacts of each small fill. Never¬
theless, the best available environmental information must be
provided, preferably in a document that clearly describes the
site and project. Certainly biologists, hydrologists, and
perhaps other scientific specialists should be involved in
obtaining and evaluating that information.

When that information shows that there is an adverse impact
that is unavoidable, it should be offset. Usually, this should
be done by reopening an area to tidal action or enhancing the
wetland values of an area that may not be sufficiently flushed
or drained or may not contain as much diversity of habitat as
biologists tell us is desirable. We have also found that it is
crucial to consult with scientists when reviewing plans to
change an area, particularly if areas are to be reopened to
tidal action, new wetland vegetation is to be established, or
other enhancement actions are to be taken.

Diked historic baylands is another recent study that in¬
volved scientific research and opinion. Prior to the Commis¬
sion's creation, substantial areas of the bay were diked off.

Many of these areas were converted to saltponds but many others
were used for hay growing, grazing, and similar agricultural pur¬
poses. These areas retain some wetland values and are often
quite important for waterfowl and other animals that use both
the Bay and uplands. Diked baylands are under pressure for
urbanization. On the other hand, they present the last opportu¬
nity to significantly improve the habitat values of the Bay.

In undertaking the diked historic baylands study, the Com¬
mission again turned to the scientific community to discover how
these areas functioned and what beneficial changes could occur.
We discovered a great deal about the species that now use the
areas, about the compatibility of agricultural and wildlife use
of many of the areas, about the difficulties of modifying such
areas, and about the flood plain and soil values of these
areas. Based on the valuable scientific information and
opinion, the Commission found that diked historic baylands had
great importance as part of the Bay system and adopted findings
and policies to use when projects were presented to the Corps.

142

Both the mitigation and diked historic bayland examples show
that governmental regulatory agencies respond well to clear,
understandable, and applicable scientific information. When the
information is in a form that the average reader can appreciate,
there is considerable public and media interest in the Bay Area.
There is an increased willingness to take the opportunity to
improve the San Francisco Bay, both through mitigation and
through increased attention to the diked historic baylands.

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147

'

THE FEDERAL ROLE IN THE MANAGEMENT OF SAN FRANCISCO BAY

Betsy Coombs

Environmental Protection Agency Region 9

I recently had the opportunity to brief the EPA's new
Assistant Administrator for Water on San Francisco Bay. I
showed him slides of the Bay, talked about declining fish
populations, reviewed the history of fisheries decline, and
talked about siltation and long-term degradation of the Bay.
During a helicopter tour of the Bay, he turned and said, "The
Bay looks so healthy!"

His reaction is not uncommon. Many of us who grew up on the
Bay are used to the idea that there are no booming fisheries on
the Bay. At one point, San Francisco Bay was the most important
fishery on the West Coast.

Despite the lack of visible causes, there are very real
problems contributing to the decline on the Bay, many of which
have been touched on today. For the first time, there is the
real possibility the EPA may receive management funds for what
we in the region recognize is a resource of national signifi¬
cance, one that deserves our attention. The budget for such an
undertaking may be $12 million, as some members of Congress have
sought, ...or it may be zero, or somewhere in between. We do not
know if our equipment will be a handful of pencils or a Prime
computer.

We are at the mercy of The Office of Management and Budget
and other people's priorities: the Congress, the State Water
Resources Control Board, the Office of Management and Budget and
the Reagan Administration. Within the next four to six months,
our sense of what the San Francisco Bay Project might be could
change by orders of magnitude and in more than one direction,
and maybe more than once or twice. But one fact is clear: EPA
Region 9 has a commitment to address the problems of San Fran¬
cisco Bay.

With that introduction, I would like to talk about EPA's
statutory role on the Bay, the Agency's relationship with other
agencies, and the establishment of EPA's National Estuaries Pro¬
gram through the creation of the Office of Marine and Estuarine
Protection.

149

Much of EPA's mandated role affecting the Bay is given under
the authority of the Clean Water Act of 1972. The Agency is
required to respond, case-by-case, to programs outlined in the
Act. The following five programs represent the majority of
EPA's activity on the Bay:

1) Under specific sections of the Clean Water Act, the EPA
is centrally involved in water quality management plan¬
ning. These activities are at the core of the basic
intent of the Act, which is to enhance water quality
and protect the public health and welfare. Section 106
allocates funds to the state for water pollution con¬
trol programs. Section 208 provided areawide water
quality management planning, and now Section 205(j)
allocates funds for specific studies and specific
problems for state water quality planning. These
programs provide important information used in setting
water quality standards, suggesting needed legislation,
and developing basin plans.

2) Under Section 303, EPA requires that the state, through
the State Water Resources Control Board, develop water
quality standards to protect the beneficial uses of Bay
waters. The state and regional boards, with public
participation, determine those designated beneficial
uses to be attained and maintained. Those uses rele¬
vant to the Bay are: municipal and industrial water
supplies, habitat for aquatic life, agriculture, and
waterways for shipping and recreation. The state has
set salinity standards for the delta and delegated the
setting of all other standards to the Regional Board.
Given that toxic pollution appears to contribute to the
declining health of the Bay, new numeric criteria need
to be established to augment the existing narrative
standards.

Under Section 301, effluent guidelines are established
for all industrial and municipal dischargers based on
Best Practicable Technology and are subject to the
standards just described.

3) Under Section 402, and subject to EPA approval, the
state issues National Pollution Discharge Elimination
System (NPDES) permits to all dischargers through the
Regional Water Quality Control Board. These permits
are the legal basis for requiring dischargers to con¬
trol the pollutant levels in their effluent. They
specify allowable levels and quality of the waste
discharge through setting specific effluent guidelines
and receiving water standards. Dischargers are moni¬
tored to determine whether they are meeting their per¬
mit conditions and to ensure that expected water qual¬
ity improvements are achieved. EPA's role here has

150

been both carrot and stick; over the past 14 years, the
EPA has provided nearly $1.3 billion to San Francisco
Bay for construction grants for sewage facilities in
the Bay area, granted under Section 201. State and
local agencies have provided the 25 percent match.

4) Under Section 404 of the Act, the Army Corps of Engi¬
neers, subject to EPA's review, issues dredge and fill
permits. A permit must be denied if the request does
not meet the series of tests set forth in Section 404.

In regard to San Francisco Bay, 404 activity relates to
the protection of seasonal wetlands, most of which are
diked. As Michael Josselyn stated earlier, 95 percent
of the Bay and Delta wetlands have already been filled
or diked. EPA requires that all efforts be made to
avoid filling any more wetlands. At the very least,
there must be no net loss, meaning that other land may
be restored to wetland. A major problem on the Bay,
however, is that there is no mitigation land available.
The so-called "available land" may be held for $300,000
to $400,000 per acre, clearly an unrealistic option.

5) EPA, under the National Environmental Policy Act
(NEPA), must review and comment on all Environmental
Impact Statements (EISs) which are required for any
agency constructing a Federal project. In contrast to
Clean Water Act mandates described above, which are
media-specific, NEPA provisions are project-specific
where water issues are just one aspect under considera¬
tion. On the Bay, EPA's role includes reviewing EISs
for construction of municipal sewer facilities, Army
Corps of Engineers proposals for navigation improve¬
ments, and Bureau of Reclamation projects to develop
water supplies.

These five areas, under the Clean Water Act and NEPA, re¬
presents EPA's primary responsibility on the Bay. As you have
noticed, each of these programs is a site-specific, project-spe¬
cific response to an action. What is missing is an understand¬
ing of the whole -- how all of these pieces fit into a larger
context.

Mike Josselyn asked me to speak specifically to the rela¬
tionship between EPA and other Federal agencies actively in¬
volved in the management of the Bay. EPA interacts in a formal
capacity with two Federal agencies: the Army Corps of Engineers
in the 404 dredge and fill permits process described previously
and the U.S Coast Guard on oil and hazardous waste spills
through EPA's Emergency Response Team. EPA also reviews EISs
submitted by any agency.

151

In addition, EPA currently works in a joint research venture
with the U.S . Fish and Wildlife Service to map the Bay's wet¬
lands. Results from this project will help us to monitor
changes in Bay wetlands over time, providing better control and
protection over that fragile 5 percent of the Bay's marshes and
seasonal wetlands that still remain.

Other agencies have carried out research on the hydrology,
chemistry, and biology of the Bay. Dominant among these, the
U.S. Geologic Survey has played a most significant role in
fleshing out our understanding of the Bay.

In summary, however, the primary responsibility for the
management of the Bay has been delegated to the State of
California, subject to EPA review under the four Clean Water Act
programs just described. Water guality standards, compliance
and monitoring, and construction grants are the primary lines of
defense for maintaining beneficial uses. As with the EPA, so
too must the state respond case-by-case, project-by-project. As
the EPA considers a management program for the Bay, it is clear
that success will depend on good coordination with state
agencies.

At the national level, the Environmental Protection Agency
has made a formal commitment to the protection of estuaries and
bays through the establishment of the Office of Marine and Estu¬
arine Protection, or OMEP, headed by Tudor Davies. Unlike many
other natural features which readily fit together under a single
national program, estuaries reguire a more holistic approach
involving the expertise, resources, and commitment of many
agencies.

We have all learned a lot today about particular characteris¬
tics of the Bay. Any program claiming to address the health
problems of this Bay must be carefully designed to meet its
unigue mix of problems. By creating OMEP, EPA has recognized
the multi-disciplinary nature of estuaries, and developed a
flexible organizational structure which can be altered to meet
the unigue needs of each estuary.

Using the Chesapeake Bay Program as a model, OMEP has de¬
signed an overall strategy for the implementation of estuarine
management programs which may be used for all significant bays.
There are five steps in their strategy:

(1) Set up a committee structure to bring in all of the
vested interested in the Bay;

(2) Identify and reach consensus on the problems and goals
of the program;

152

(3)

Implement a data management program to collect all
available data bases in one system and make the results
available to all Bay researchers;

(4) Identify data gaps and conduct needed research to
develop a comprehensive understanding of the estuary;
and

(5) Adopt a management plan for the restoration of the
estuary.

It is useful here to note that EPA can undertake this
management role successfully with no new legislation; our
current authority is sufficient.

Under the leadership and guidance of OMEP, three programs
have been started in the east -- Long Island Sound, Narragansett
Bay, and Buzzards Bay, as many of you are aware. The program
has moved westward in introducing a program on Puget Sound. If
given the opportunity, EPA Region 9 stands ready to implement
such a program for the San Francisco Bay and Delta Bay, and we
would look to OMEP for guidance through their established track
record on the five other estuaries.

You have heard a good deal today on the research that has
been done to understand specific aspects of the Bay system.
Resarch has revealed problems in the Bay, symptoms that reflect
complex interrelationships that have not been well defined.
Nowhere is there an overview of the Bay system as a whole. The
Bay needs a team effort and the commitment of agencies to work
together in understanding their estuarine ecosystem and
implementing a management plan to protect it. We at EPA are
excited about being a central part of this effort, and we look
forward to working with the many agencies and organizations that
have played a critical role on the Bay and that have a stake in
its future.

153

'

CALIFORNIA REGIONAL WATER QUALITY CONTROL BOARD

SAN FRANCISCO BAY REGION

ROGER B. JAMES, EXECUTIVE OFFICER

The State of California's water quality management system is
unique, has a relatively long history and frequently amazes
those that visit us from other states and countries. The system
for managing wastes in the San Francisco Bay Area includes over
100 counties, cities, and special districts responsible for
sewerage service with the State providing the regulatory
framework for protection of surface and ground waters.

During the mid-1960s, the State undertook a comprehensive
study of San Francisco Bay and the Delta systems to develop a
long-range plan for management of the Bay Area's municipal and
industrial wastes and agricultural drainage from the Central
Valley. This study recommended ocean disposal of the Bay Area's
wastes after primary treatment at a facility in San Mateo
County, numerous studies to assess the biostimulatory and toxic
impacts of waste discharges, and a regional agency to implement
the long-range plan. Opposition to the plan and concern about
the loss of local authority led to 13 subregional planning
studies controlled by the agencies responsible for sewerage
service. A number of joint power authorities were formed to
conduct the studies and construct over $2 billion in treatment
facilities and deepwater outfalls into the Bay system.

The California Regional Water Quality Board-San Francisco
Bay Region (RWQCB) is the State Agency with the responsibility
for the protection of surface and ground water quality in the
nine Bay Area counties. The RWQCB has been in operation since
1950 and is one of nine such agencies in the State of California
with the authority and responsibility to implement the State
Porter- Cologne Water Quality Control Act and the Federal Clean
Water Act (FWCA).

The RWQCB operates under statewide policies of the State
Water Resources Control Board (SWQCB) which provides budget
control, considers appeals of RWQCB actions, adjudicates the
State's water rights programs, and administers the Federal con¬
struction grant program. The RWQCB implements its responsibl-
iities through four fundamental programs: basin planning, waste
discharge requirements including the Federal NPDES permits sur¬
veillance and monitoring and enforcement.

The nine members of the RWQCB are appointed by the Governor
for staggered four year terms which provides for relative inde¬
pendence and continuity of actions. The RWQCB is supported by a

155

full-time technical staff responsible for implementation of its
policies and regulations. The RWQCB's independence combined
with a requirement that all planning and regulatory decisions be
made in public following quasi-judicial hearings to assure a
degree of consistency and predictability and has resulted in a
high degree of public acceptance of its decisions.

People living in the San Francisco Bay have a very strong
environmental awareness and concern about the pollution of
ground water and San Francisco Bay. In spite of earlier testi¬
mony at this seminar, the greatest public concern is with ground
water contamination problems in the Silicon Valley from leaking
underground tanks. In this area, there are 120 sites where
solvents have contaminated ground water and over 3 00 motor fuel
tanks with leaking gasoline tanks. The RWQCB regulates over 450
discharges including 43 major municipalities, 19 major indus¬
tries, and 16 onsite and offsite discharges are non-hazardous
waste landfills, smaller municipalities and industries and agri¬
cultural operations. In addition to these discharges, there are
115 dairies and 15 wineries regulated through an exempting
process.

POLICY AND MANAGEMENT DECISIONS

A number of major policy and management decisions have
influenced water quality control and beneficial uses in the Bay
area and perhaps the most significant was the political decision
in the late 1960s to not form a regional agency with the author¬
ity to implement Bay- Delta Plan. The next critical decision
influencing the Bay was the 1972 amendments to the FWCA that
mandated best available technology for treatment of municipal
and industrial wastes. These requirements combined with the
availability of State and Federal construction grants up to
87 1/2 percent for local agencies resulted in the consolidation
of 82 municipal treatment plants into 49 large systems with
upgraded treatment. Over one-third of the total municipal flow
now receives tertiary treatment achieving a 70 percent reduction
since 1960 in the wasteloading of conventional pollutants such
as BOD, SS, and oil and grease in spite of a 100 percent
increase in flow. The extreme South Bay has experienced the
most dramatic reduction of over 90 percent of these pollutants.
The record for major industries is even more impressive with
volumes of flow reduced by three-fourths and conventional
pollutants reduced by over 95 percent since 1960. Although
comparative data is limited, there is evidence that the dis¬
charge of toxic pollutants, such as heavy metals and organic
chemicals, have been significantly reduced from both industries
and municipalities. Heavy metal loadings estimated at 8 million
pounds a year in the 1960s have reduced by over 90 percent.

156

Other major decisions that have affected the protection of
San Francisco Bay and the adjacent wetlands have been the
formation of the Bay Conservation and Development Commission
that limited further filling of the Bay; the RWQCB's support of
State and Federal fisheries agencies policies regarding "no net
loss of wetlands in the regulation of landfills;" the Citizens
for a Better Environment pressure to implement the Federal
pretreatment programs to reduce toxic materials discharged to
municipal sewerage systems; and the RWQCB's pursuit of best
management practices to prevent the spill of petroleum products
during vessel transfer operations.

These decisons have resulted in the re-establishment of
beneficial uses such as the opening of 1 mile of shoreline in
San Mateo County for the public harvesting of shellfish in 1982,
1983, and 1985 for the first time since the 1930s; the consid¬
eration of commercial oyster and clam farming along the East Bay
shoreline; and, the extreme South Bay, once grossly polluted,
now supports a commercial bait shrimp fishery and there are
reports of sturgeon and striped bass being caught. Less subtle
improvements have been the increased water clarity and reduced
bacterial levels along the San Francisco shoreline as a result
of the reduction of wet weather raw sewage combined sewer
overflows from 80-100 to several each year.

Many of these management decisions were mandated by the
FWPCA, were made possible as a result of the availability of
sewage construction grants and resulted from the public's con¬
cern about gross pollution caused by such incidents as oil
spills. Although there have been success stories as a result of
these management decisions, there is growing concern about toxic
discharges to the Bay; impacts on non-point sources such as
urban runoff, dredging, and spoil disposal; agricultural drain¬
age containing selinium and pesticides; and impacts of further
diversions of freshwater which is considered to be necessary for
the maintenance of a balanced estuarine system.

WATER QUALITY MANAGEMENT NEEDS

The water quality management needs of San Francisco Bay are
numerous and varied ranging from completion of the already plan¬
ned improvements to waste water facilities to basic research on
those factors affecting Bay water quality. The City and County
of San Francisco need to construct approximately $400 million in
sewer system improvements to complete essential elements of its
Master Plan and the East Bay Cities are faced with expenditures
up to $750 million to upgrade the sewer systems to reduce raw
sewage overflows.

157

The greatest need is to significantly expand and better
coordinate the data collection, analysis, long-term monitoring
and research conducted on the Bay. An adeguate and consistent
funding source has been the major problem in meeting this need
and the Bay Area citizens must provide this funding source
independent of State and Federal funding which are too variable
and subject to budget constraints.

The second most important need is to establish an insti¬
tution with a core of experts doing basic and long-term research
on the Bay. It is essential that the institution have the abil¬
ity to coordinate all research efforts in the Bay as well as
maintain a knowledge of current research underway in similar
estuaries throughout the world. This institute should be funded
and be capable of responding to and investigating the causes of
incidents such as the Mesodinium Rubrum blooms that occurred
during the late 1960s and the San Pablo Bay Cladophora bloom in
1979. The institute should also provide expert testimony to the
SWRCB and RWQCB to assist in their regulatory decisions. The
Aquatic Habitat Institute established by the SWRCB is the most
viable organization to satisfy this need.

The third major need is to establish a system or mechanism
to span the information gap between the research/data collection
efforts and the public's knowledge on the condition of the Bay.

The Bay Area problems listed water pollution as second only be¬
hind transportation. One of the most difficult questions faced
by the RWQCB staff is the condition of the Bay and what actions
are needed to protect the Bay.

The list of resource management needs are virtually endless
and the potential for public harvest of shellfish is just one
example of a beneficial use that can be expanded.

The greatest regulatory management need is the development
of water quality based standards for species indigenous to the
Bay, including the most sensitive. The technology based
standards mandated by the FWPCA have been implemented in the Bay
Area, yet there is growing evidence that these standards are
inadequate to protect beneficial water uses identified by the
RWQCB. We must rapidly move forward to develop these standards
based on the best available information.

In summary, considerable progress has been made during the
past 25 years to reduce pollutants discharged into San Francisco
Bay in response to the California Water Code and FCWA; however,
there is evidence that the San Francisco Bay system and benefi¬
cial uses are stressed and adversely impacted. Toxics in muni¬
cipals and industrial discharges, non-point source discharges,
water diversions, pollutant input from the Delta, dredging, and
toxic spills are factors that affect San Francisco Bay.

158

One major problem in assessing the relative importance of
these factors is a fundamental lack of understanding of the
complex relationships between pollutant discharges, Delta out¬
flow, and the health of the biological community of San Fran¬
cisco Bay. This lack of understanding, rather than shortcomings
in the law or its implementation, is now the major impediment to
the RWQCB in carrying out its mandate to protect the quality of
the waters of San Francisco Bay.

The solution to this problem is a sustained program of
research on the physical, chemical, and biological processes
that affect the Bay.

159

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