FUTURE FISHERIES IMPROVEMENT

PROGRAM

REPORT TO 2001 LEGISLATURE

AND
FISH, WILDLIFE AND PARKS COMMISSION

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1 420 East 6th Avenue

P.O. BOX200701

Helena, MT 59620-0701

Prepared by:

Habitat Protection Bureau

Fisheries Division

SWTE DOCUMENTS COLLECTION

MAR 1 3 2001

MONTANA STATE LIBRARY

1515 E. 6th AVE.
HELENA, MONTANA 59620

December 2000

MONTANA STATE LIBRARY

3 0864 0015 6908 9

Digitized by the Internet Archive

in 2010 with funding from

Montana State Library

http://www.archive.org/details/futurefisheriesi2000mont

CONTENTS

Page

Program Summary & 1

Project Funding and Status (Table 3) 5

Photos of Typical Projects 17

Project Descriptions 22

Appendix A — Monitoring Report

Table of Contents A-ii

List of Tables A-iii

Introduction A-l

Project monitoring by drainage A-l

Acknowledgments A-46

References A-46

Cover photo: Aerial photograph of Big Spring Creek (near Lewistown) showing a newly
constructed meandering channel on the Brewery Flats Fishing Access Site. The old channel
(parallel to the road) was straightened when the railroad was built near the turn of the century.
Stream length as a result of the project will increase from 2,600 to 3,950 feet.

MONTANA FISH, WILDLIFE AND PARKS
Fisheries Division

Future Fisheries Improvement Program

And

Bull Trout and Cutthroat Trout Enhancement Program

Summary 1995-2000

The Future Fisheries Improvement Program (HB 349) provides funds for: "the long term
enhancement of streams and stream banks, in stream flows, water leasing, lease or purchase of
stored water, and other voluntary programs that deal with wild fish and aquatic habitats. " The
Future Fisheries Improvement Program was supplemented in 1999 when the legislature enacted
the Bull Trout and Cutthroat Trout Enhancement Program (HB 647) which "provides for the
enhancement of Montana bull trout and cutthroat trout populations through voluntary
enhancement of spawning areas and other habitats for the natural reproduction of bull trout and
cutthroat trout. "

This report summarizes project funding and status of all projects that have been approved since
these programs began in 1995 and 1999, respectively. The report also includes a brief narrative
description of all projects approved since the last reporting period. Results of project monitoring
are summarized in Appendix A.

Review Panel: Panel members during this report period included: Jim Stone, representing the
North Powell County Conservation District, Ovando; Roy Gabel, commercial rancher, Huntley;
Doug Parrott, commercial rancher and irrigator, Roundup; Paul Callahan, Land and Water
Consulting, Aquatic Habitat Consultants, Missoula; Duane Phinney, fishery biologist, St. Regis;
Robert Twiford, licensed angler, Malta; Earl Dorsey, licensed angler, Helena; Nick Morales,
student, Capital High School, Helena; Senator Jack Wells, Bozeman; Representative Dan
Fuchs, Billings; Dr. Steve Custer, hydrologist, Montana State University, Bozeman; Greg
Watson, Plum Creek Timber Company, Missoula; and Gordon Stockstad (ex-officio), Montana
Department of Transportation. The review panel met four times since the last report — January
99, July 1999, January 2000, and July 2000. Project proposal deadlines are January 1 and July 1
of each year.

Staffing: Mark Lere has been the Program Officer since November of 1 997. Mark is
responsible for reviewing project applications, visiting the sites of proposed projects,
communicating department recommendations to the review panel, completing MEPA
requirements, coordinating with consultants and contractors who design and perform restoration
projects, developing project proposals, and working with landowners and other citizens who need
help developing proposals.

Other program staff include Brad Shepard (0.5 FTE, biologist) who is responsible for project
monitoring. Brad maintains a database to track restoration project monitoring conducted by

1

other biologists and conducts field monitoring of approximately 15 projects. His monitoring
report is attached (Appendix A). Eric Reiland (0.5 FTE, biologist) is responsible for working
with landowners to develop projects west of the Continental Divide. Eric is presently working in
the upper Clark Fork and Rock Creek drainages. Lee Nelson (0.5 FTE, biologist from HB 647) is
responsible for cutthroat restoration efforts in the Elkhorn Mountains. Glenn Phillips, Chief of
the Habitat Protection Bureau, continues to be responsible for overall program administration.

Operating Budget: Operating expenses during FY-99, FY-00, and FY-01 are summarized in
Table 1.

Table 1.

2000.

Future Fisheries Improvement Program operating expenses July 1, 1998-October 31,

Expense category

FY-99

FY-00

FY-01

Salaries and Benefits

85,630

94,737

32,938

Operating Expenses

Services

384

4,134

188

Supplies & Materials

5,513

2,182

1,462

Communications

1,077

1,153

353

Travel

12,179

9,508

5,591

Repair & Maintenance

392

299

266

Education and Training

1,130

690

65

Miscellaneous

980

989

380

Total

107,285

113,692

41,243

Anticipated Expenses: House Bill 349 requires Fish, Wildlife and Parks to report "anticipated
expenses for the ensuing 10 years implementation of the program." During the first five years of
the program, we have committed, on average, about $0.7 million/yr to projects. There are
approximately $1.0 million of uncommitted dollars remaining in the program budget.
If $350,000 (the average committed per funding cycle to date) is allocated to projects during the
January 2001 funding cycle, there will be about $650,000 in program dollars that will carry
forward into the next biennium and which will be added to the $2.01 million that is in the
Governor's budget for the next biennium. Over the next ten years we anticipate continuing to
spend approximately $1.5 million per biennium or about $7.5 million over the next ten years.

Projects and appropriations: To date the Future Fisheries Review Panel and Fish, Wildlife and
Parks Commission have fully or partial funded 237 projects. Additionally, both the review panel
and the commission approved funding for the Tongue River project. The 1995 legislature
earmarked $510,000 for projects to enhance fisheries in the Tongue River; an additional
$275,000 was appropriated towards this purpose by the 1999 legislature. These projects are to
partially mitigate for fishery losses associated with the construction of Tongue River Dam. The
Tongue River projects are administered by the state of Montana, the Northern Cheyenne Tribe,
and the United States Bureau of Reclamation.

Legislative appropriations to the Future Fisheries program include: 95-$2,270,000; 97-
$1,385,000; 99-1,470,000; Total-$5, 125,000. Additionally, the 1999 legislature appropriated
$750,000 from our general license account and $500,000/yr (beginning in 2001) from the
Resource Indemnity Trust Account to the Bull Trout and Cutthroat Trout Enhancement Program.

Table 2. Summary of projects approved, program dollars committed, and matching dollars
committed during each funding cycle.

Funding

Projects

Program $

Matching $

Cycle

Approved

Committed

Committed

Winter 96

30

$666,601

$1,722,289

Summer 96

18

164,278

172,416

Tongue River (96&99) 1

785,000

115,000

Winter 97

27

435,807

767,052

Summer 97

18

266,617

1,677,408

Winter 98

23

320,520

712,300

Summer 98

26

483,397

410,187

Winter 99

20

360,860

571,981

Summer 99

30

379,114

937,735

Winter 00

30

285,847

1,049,606

Summer 00

14

206,298

200,847

Total

237

$4,347,868

$8,336,821

The process for securing the financial involvement of the Montana Department of Transportation
in bull and cutthroat trout enhancement projects, as outlined in HB 647, is continuing to evolve.
The Department of Transportation is a willing participant but projects must be located in areas
where new roads are being constructed. Further, restoration projects must be scheduled
concurrently with road construction. Several restoration projects are underway or are presently
being planned including reaches of Camp Creek south of Hamilton, Kleinschmidt Creek near
Ovando, and Therriault Creek near Eureka. We are also working toward mitigation agreements
along transportation corridors where bull and cutthroat trout occur; mitigation funds will
potentially be available for bull and cutthroat trout habitat restoration projects.

Table 3 summarizes the budget and status of projects that have been approved to date. Thirty of
the approved projects are to improve fish habitat in lakes, reservoirs or ponds and the remaining
projects are for habitat improvements in rivers and streams. Bull trout and cutthroat trout projects
funded through HB 647 are highlighted in Table 3.

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Photo Illustration 1. Restoration of a side channel on the Stillwater River
located near the town Absarokee. This abandoned side channel was restored to
provide additional spawning and rearing habitat for rainbow trout and brown
trout. Upper photo shows side channel during construction. Lower photo shows
restored side channel following construction.

17

AFTER

8/28/00
1 2 cf s flow

3W

Photo Illustration 2. Instream flow restoration in lower Big Creek, a tributary to the Yellowstone
River located near the town of Emigrant. The program provided funding to allow landowners to
convert to more efficient sprinkler irrigation, creating salvage water for two instream flow leases.
This instream flow provides spawning and rearing habitat for Yellowstone cutthroat trout. Note large
rock in channel of stream for photo reference.

IS

Photo Illustration 3. Esp/Chamber Spring Creek, a tributary to the Yellowstone River
located near the town of Big Timber, before (upper photo) and after (lower photo) restoration.
Note the telephone pole for reference. The project involved channel reconstruction, riparian fencing,
off-channel water development for livestock and replacement of a perched culvert. Yellowstone
cutthroat trout have been introduced to promote future use as a spawning and rearing tributary.

19

•i^k

A,**'

Photo Illustration 4. Canyon Creek, located north of Helena, during (upper photo) and
after (lower photo) channel restoration. This project involved channel re-construction
and riparian fencing undertaken to improve habitat for resident rainbow trout, brown
trout and brook trout.

20

Photo Illustration 5. (Top photo) Installation of a fish screen into a diversion on Little
Prickly Pear Creek, a tributary to the Missouri River located north of Helena. Little
Prickly Pear Creek is an important spawning tributary for migratory rainbow trout and
brown trout from the Missouri River. (Bottom photo) Wind powered aerator installed on
Salmo Reservoir located in Blaine County to prevent winter-kill of bass and bluegill.

21

Project Descriptions-1999

1. Big Hole flow enhancement. Big Hole River (Beaverhead County) near Wisdom suffers
from seasonal dewatering. Diverted water is used primarily for stock watering. This reach of the
river supports the last remaining population of fluvial arctic grayling in the lower 48 states. This
project is part of a larger effort to provide off-stream watering and improve Big Hole River
stream flows. Monies were used to construct a power line to the well site to operate the pumps.
Ranchers have agreed to leave the diverted water in stream (20-30 cfs) in exchange for the
development of the off-stream watering. Completed.

2. Big Hole flow enhancement. Big Hole River (Beaverhead County) near Wisdom suffers
from seasonal dewatering. This project supplements project #1 above. Project dollars were used
to develop two springs for off-stream watering of cattle. This is part of a larger project to
increase Big Hole River stream flows. Ranchers have agreed to leave diverted water in stream
(20-30 cfs) in exchange for the development of the off-stream watering.

3. Butler Creek riparian enhancement. Butler Creek (Missoula County) had become degraded
over the years due to livestock trampling. Butler Creek supports a pure strain population of west
slope cutthroat trout. This project involved riparian fencing to allow streamside areas to recover
and off-stream water development. Approximately 500' of stream was treated. Completed.

4. Bynum Reservoir spawning structures. Bynum Reservoir (Teton County) supports a
popular yellow perch fishery but numbers are limited due to a scarcity of spawning habitat and
rearing cover. Several types of spawning structures were previously placed in the lake; scotch
pines appeared to work best because of their dense network of branches. The project involved
placing an additional 550 scotch pine structures in the lake. Completed.

5. Camp Creek restoration. Camp Creek (Ravalli County); a tributary to the East Fork of the
Bitterroot River was channelized many years ago when the highway was constructed. The stream
supports populations of cutthroat and brook trout. This project involves returning the stream to
its historic channel and reconstructing the channel to simulate its natural stable form.
Approximately two miles of stream will be reconstructed. Additionally, wetlands are being
developed on adjoining lands. This project is being jointly funded between FWP and the
Montana Department of Transportation.

6. Coal Creek fencing. Coal Creek (Ravalli County), a tributary to the West Fork of the
Bitterroot River, supports populations of both bull and cutthroat trout. The stream was damaged
by grazing. The project involved construction of approximately 1 mile of jackleg fence to
exclude cattle from approximately 0.5 miles of stream. Completed.

7. Cottonwood Creek bank stabilization. Cottonwood Creek (Fergus County) supports both
brown and brook trout populations. Previous grazing damaged the stream. However, the

22

applicant recently fenced the riparian area to exclude livestock. This project involved stabilizing
approximately 200' of a high eroding bank using back sloping, rock veins, sod mats, willow
clumps, and root wads. Completed.

8. Douglas Creek fish passage. Douglas Creek (Powell County), located on the Manley Ranch
near Helmville, supports pure strain westslope cutthroat trout populations. Three irrigation
reservoirs prevent movement offish throughout the system. This project will establish fish
passage throughout the system and improve population viability and recruitment.

9. Elk Creek restoration. Elk Creek (Lewis and Clark County) located near Augusta, supports
a significant spawning run of brown and rainbow trout from the Sun River. This project on the
Scherrer Ranch involved treating eroding banks using root wads and willow plantings and
narrowing and deepening the channel; approximately 2,300' of stream was treated. Completed.

10. Flat Willow Creek restoration. The project was approved but the ranch changed hands and
the funding request was subsequently withdrawn. Withdrawn.

1 1 . Horseshoe Lake boulder clusters. Horseshoe Lake (Lake County) supports a popular
fishery for smallmouth bass. However spawning and rearing habitat appears to be limited. This
project will involve placement of boulder clusters to provide spawning and rearing habitat.

12. Prickly Pear Creek restoration. Prickly Pear Creek (Lewis and Clark County) near its
confluence with Lake Helena supports brown and rainbow trout populations. The stream had
become degraded over the years due to grazing and irrigation practices. The new owners are
interested in improving the stream and also allow public fishing. The project included restoration
of approximately 5,800' of stream using a variety of techniques including back sloping and
revegetation, rootwad revetments, sod mats, rock vanes, channel shaping, and riparian fencing.
Completed.

13. Rock Creek flow enhancement and restoration. Rock Creek (Powell County) is a
tributary to the Clark Fork River near Garrison. Rock Creek has potential as a spawning stream
for Clark Fork River fish but the lower 2.5 miles was historically dewatered due to irrigation.
The dewatered reach also lacked habitat complexity. This project involved installation of a more
efficient irrigation system and using the salvaged water for instream purposes (a minimum of 5
cfs). The project also included restoration of the lower 2.5 miles of stream and elimination of a
migration barrier. Completed.

14. Ruby River feed lot relocation. The Ruby River (Madison County) is one of Montana's
most popular trout streams. A feedlot located on the Sauerbier Ranch is located immediately next
to the stream and has flooded several times in recent years due to upstream diking to protect the
town of Alder. This project involves moving the feedlot away from the stream to prevent animal
waste from being flushed into the Ruby.

23

15. Smith River and Thompson Creek fencing and off-stream watering. Smith River
(Meagher County) and Thompson Creek located on the Brian Bodell Ranch are damaged due to
grazing practices. This project involves riparian fencing and off-stream water development to
improve the health of approximately 1 .3 miles of Thompson Creek and 4.2 miles of the Smith. R

16. Sun River bank stabilization. Portions of the Sun River (Cascade County) between Fort
Shaw and Sun River suffer from erosion due to adjacent land management practices. An
inventory of this reach was completed two years ago to identify problem reaches in need of
correction. This project involved treatment of two of these reaches (1 ,500' total) and included
back sloping, root wads, and fencing to stabilize eroding banks. Completed.

1 7. Ten Mile Creek revegetation. Ten Mile Creek (Lewis and Clark County) has been
degraded by roading and adjacent land management activities. This project involved planting
willows, trees and shrubs along streamside areas to improve riparian condition. Approximately
3,500' of stream was treated. Completed.

18. Warren Creek restoration, fencing and fish passage. Warren Creek (Powell County) is a
second order tributary to the Blackfoot River near Ovando. The stream supports cutthroat as
well as brown and rainbow trout. The stream was historically channelized, woody vegetation
removed, the stream routed through the corrals, and an irrigation diversion was installed that is a
barrier to fish migration. This project includes complete restoration of 1 .5 miles of stream,
installation of 1.5 miles of riparian fencing, installation of a new diversion fitted with a fish
ladder, and replacement of the old corral with an off-stream corral.

19. South Fork of Lower Willow Creek riparian fencing and revegetation. The South Fork
of Lower Willow Creek (Granite County), which supports a pure strain population of cutthroat
trout and bull trout, has been damaged over the years due to uncontrolled livestock grazing. This
project involved installation of 4.6 miles of fencing, and development of a grazing management
plan designed to protect the stream. Willows were planted in riparian areas to speed the
recovery. Completed.

20. Huntley diversion fish passage. The Huntley Irrigation Diversion on the Yellowstone
River near Huntley (Yellowstone County) has been a fish migration barrier for many years.
This project involved installation of a rock fishway during a period when the dam was repaired
for flood damage. Hopefully, the fishway will allow fish to migrate past the diversion structure.
The Bureau of Reclamation is presently monitoring passage success. Completed.

21. Bad Canyon Creek rehabiliatation (BT-CTT). Bad Canyon Creek (Stillwater County) is a
tributary to the Stillwater River. The stream supports a native population of Yellowstone
Cutthroat Trout as well as non-native brown trout that compete with the native cutthroat. The
upper reach of the stream includes a waterfall that acts as a natural migration barrier for
downstream fishes. The project involves only the reach of stream located above the waterfall.
This project involves removing and safely holding the cutthroat, treating the stream with

24

antimycin to eliminate the brown trout, and returning the cutthroat to the stream. This project
will allow the native cutthroat population to expand without competition from non-native fishes.
The project is a joint effort between the BLM, USFS, and FWP.

22. Poindexter Slough protection. Poindexter Slough (Beaverhead County) is one of the few
spring creeks in Montana that is in public ownership. The Slough supports one of the highest
densities of brown trout in the state and provides important recruitment to the Beaverhead. This
project involved installing a grade control to prevent the Beaverhead River from capturing the
spring creek. If capture were to occur, about three miles of Poindexter Slough and several miles
of the Beaverhead River would be negatively affected. Completed.

23. Big Coulee Creek barrier (BT-CTT). Big Coulee Creek (Choteau County) supports a
remnant, pure population of west slope cutthroat trout. This projects involves creation of a
migration barrier to protect the genetic integrity of this population and prevent invasion by non-
native brook trout.. The project is located on the Lewis and Clark National Forest.

24. Canyon Ferry spawning structures. Canyon Ferry Reservoir (Lewis and Clark and
Broadwater Counties) supports a popular fishery for yellow perch. Perch are also an important
forage for walleye. Brush and Christmas tree structures have been used in the past to try and
enhance spawning and rearing habitat for yellow perch. This project expanded that effort.
Completed.

25. Clark Fork fencing and revegetation. A 600 ft reach of the Clark Fork River near Clinton
suffers severe bank erosion due to past grazing practices. This project would have included
stabilizing the bank using soft techniques, revegetating with dogwood and willow clumps, trees
and sprigs. The treated area would have been fenced and managed as a grazing exclosure.
Cancelled.

26. Cottonwood Creek barrier (BT-CTT). Cottonwood Creek (Lewis and Clark County) on
the Beartooth Game Range is a candidate site for re-establishing a pure population of westslope
cutthroat trout. The upper six miles of stream presently supports a mixed population of cutthroat,
brook, and rainbow trout. This project involves construction of a barrier that will isolate the
upper six miles of stream. Once the barrier is in place, the competitors will be removed and the
cutthroat population re-established.

27. Cottonwood Creek fish passage and grazing management (BT-CTT). Cottonwood Creek
(Powell County) is a cutthroat stream in the Blackfoot River drainage. This project includes
repair of a fish ladder, replacement of a culvert to enhance fish passage, and implementation of a
grazing management plan along 0.6 miles of stream.

28. Daisy Dean Creek off stream watering and fencing (BT-CTT). Daisy Dean Creek (Park
County) is a tributary to the Shields River near Wilsall. Daisy Dean Creek supports brown trout
and Yellowstone Cutthroat. This project involved off-stream water development, fencing, and
development of a grazing management plan. Completed.

25

29. Elk Creek restoration. Elk Creek (Lewis and Clark County) near Augusta has been the site
of several stream restoration projects. This project involved restoration of 2,100 ft of stream on
the Artz Ranch that had been damaged by grazing practices. Treatments included narrowing the
channel, pool development, bank shaping, willow plantings, and placement of root wads and tree
revetments. Completed.

30. Grave Creek diversion repair and fish screen (BT-CTT). Grave Creek (Lincoln County)
supports runs of both bull trout and cutthroat trout from Libby Reservoir. An existing irrigation
diversion captures migrating fish. This project includes installation of a fish screen on the
diversion structure, removal of a log diversion dam and installation of a series of smaller rock
wiers, and removal of bedload that has accumulated behind the diversion.

31. Rock Creek and Kleinschmidt Creek water lease. Rock and Kleinschmidt Creeks (Powell
County) are spring fed tributaries that enter the North Fork of the Blackfoot River near Ovando
and were historically used by bull trout. Both streams are subject to ongoing restoration efforts.
This project involves leasing 15 cfs of salvaged water on the John Krutar property and will
prevent upstream landowners from claiming the water for consumptive purposes; the lease would
be for 1 0 years.

32. Little Prickly Pear Creek fish screen. Little Prickly Pear Creek (Lewis and Clark County)
is an important spawning stream for Missouri River rainbow trout. Brown trout and whitefish
are also present. An irrigation diversion ( Sieben/Wirth) previously captured out-migrating adult
and juvenile fish. This project involved installation of a fish screen on the diversion.
Completed.

33. Little Prickly Pear Creek fence and stockwater. Little Prickly Pear Creek (Lewis and
Clark County), on property recently acquired by the Oxbow Ranch, has been damaged by past
grazing practices. This is an extremely important rainbow trout spawning stream for the
Missouri River. This project involves installation of fencing and off-stream water development.
Approximately 2 miles of stream will be protected.

34. Lost Creek Corral relocation. Lost Creek (Deer Lodge County) is a tributary to the Clark
Fork River near Warm Springs. Portions of Lost Creek on the Ueland Ranch support nice
populations of brown trout while others reaches have been heavily damaged by grazing. An
effort is under way to try and restore the entire 6. 1 mile reach of Lost Creek. This project (phase
II of the restoration effort) includes relocation of a corral facility, offstream water development,
and development of a riparian management plan.

35. Middle Fork Rock Creek riparian fence (BT-CTT). Middle Fork Rock Creek (Granite
County) is a bull trout spawning stream that has been damaged by grazing. This project includes
installation of 1 .6 miles of fencing and two cattle guards. This project will eliminate cattle
access to 12 miles of Copper Creek (a tributary to the Middle Fork) and 8 miles of the Middle
Fork.

26

36. Monture Creek restoration (BT-CTT). Monture Creek (Powell County) provides
spawning and rearing habitat for bull trout and westslope cutthroat trout. Poor grazing and
riparian management have degraded the stream on the Heart-bar-Heart Ranch. This project
involved restoring approximately 4,000 ft of stream using log veins, large woody debris and
rootwads, and shrub plantings. A grazing management plan was developed to protect the stream.
Completed.

37. Ninemile Creek restoration and fencing. Ninemile Creek (Missoula County) is a tributary
to the Clark Fork River downstream of Missoula that supports a variety of trout species. The
Creek on the Denim property has been damaged by previous grazing practices. This project
involves riparian fencing to exclude livestock from 1.75 miles of stream and treatment of eroding
banks using natural materials. The property is being placed in a conservation easement.

38. 0,Brien Creek grade control. O'Brien Creek (Missoula County), a tributary to the
Bitterroot River near Missoula supports a mixed trout population including westslope cutthroat
trout. The stream has been the site of previous habitat restoration work. During the 1999 high
water period, a headcut developed in the lower reaches. This project included installation of
three log and rock vortex weirs to prevent further head cutting and planting of about 200 native
shrubs in stream side areas. Completed.

39. Habitat improvements (BT-CTT). Pearson Creek (Powell County) is a tributary to the
Blackfoot River and is an important spawning tributary for cutthroat trout. Riparian areas have
been degraded under previous ownership due to poor land management practices. This project
included riparian fencing to exclude livestock, development of off-stream watering, placement of
woody debris to add channel diversity, planting of riparian shrubs and channel improvement s at
a stream crossing. Approximately 3000 ft of stream was treated. Completed.

40. Prospect Creek channel restoration (BT-CTT). Prospect Creek (Sanders County) is a
tributary to the Clark Fork River near Heron. The stream has become degraded over the years
due to construction of roads and pipelines and removal of riparian vegetation. The stream
supports a mixed trout population including westslope cutthroat and bull trout. This project will
treat approximately 3 miles of stream. The goal of the project is to recreate a stable bank full
channel and functioning floodplain. Treatments will include intensive revegetation; bank
stabilization using rootwads, rock, and native material revetments; floodplain grade controls and
brush bars to limit sediment delivery to the channel; and channel shaping to restore the natural
dimensions and facilitate sediment and bedload transport.

41 . Racetrack Creek riparian fence. Racetrack Creek (Deer Lodge County) supports a mixed
trout fishery that is dominated by brown trout. The reach of stream where this project was
completed was damaged by previous grazing. A channel restoration project had already been
completed and this project involved construction of 1.2 miles of riparian fencing to protect the
restoration investment. Completed.

27

42. Ronan Spring Creek channel restoration. Ronan Spring Creek (Lake County) and
tributaries have been the site of several previous stream restoration projects. This project
restored an untreated reach that flows through the city park and an adjacent property that was
degraded by a variety of land use activities. The project involved narrowing and deepening the
stream and returning it to a single channel. Completed.

43. Salmo Reservoir aerator. Salmo Reservoir (Blaine County) is a small impoundment that
used to support a wild bass/bluegill fishery. However, low oxygen levels in winter and
subsequent winter kills have eliminated all but catfish from the reservoir. This project involved
installing an aeration system that will allow winter survival and sustainance of a wild fishery.
Completed.

44. Shields River bank stabilization. Shields River (Park County) supports a mixed trout
fishery. Stream banks in the project area were overgrazed and eroding. Previous attempts by
landowners to stabilize the banks added to the problem. This project involved treating selected
locations along 1,830' of bank using rootwads and rock veins. A section of channel around an
island was returned to a single channel, a grade control installed, and two irrigation diversions
replaced. Measures were also taken to prevent Cole Creek from capturing the stream.
Completed.

45. Shields River channel rehabilitation. Shields River (Park County) supports a mixed trout
fishery, including Yellowstone cutthroat trout. Stream banks have been degraded by grazing
practices and past attempts at stabilization. This project involves treating approximately 600' of
stream banks using rootwads, tree revetments, and willow clumps. Also, portions of the channel
will be realigned. Riparian fencing and off-stream water development will be used to protect the
treated bank as well as an additional 0.75 miles of stream. Landowners on both sides of the
stream are committed to changing management practices to protect the stream.

46. South Fork Smith - off site water and fence. The South Fork of the Smith River (Meagher
County) supports a mixed trout fishery. The stream has become degraded over the years due to a
variety of land use activities. This project involves installation of riparian fencing and
development of off-stream watering. The riparian pasture will be managed to promote improved
woody vegetation and riparian condition. Approximately 6,000 ft of stream will be treated.

47. Spring Creek fish barrier. Spring Creek (Madison County) on the John Malesich Ranch
supports a pure strain population of westslope cutthroat trout. This project involves installation
of a barrier to protect the genetic integrity of this population. The applicant has agreed to
maintain the structure once it is installed.

48. Spring Creek restoration. Spring Creek (Lewis and Clark County) enters the upper
Blackfoot River near Lincoln. The creek flows through a subdivided area and is degraded
primarily from small impoundments built along the stream and replacement of riparian
vegetation with lawns. Because of the above, the stream has become overly widened in some

28

reaches. This project involves restoring approximately 6,600 ft of channel using a variety of
treatments including channel narrowing, bank construction, willow transplants, willow sprigging,
willow facines, and placement of erosion control fabric and sod.

49. Staubach Creek native fish protection. Staubach Creek (Broadwater County) supports a
population of pure strain westslope cutthroat trout. A migration barrier has already been
installed on the creek to prevent invasion of rainbow trout and subsequent hybridization. This
project involved repairing a leaking irrigation flume that carries Beaver Creek water over
Staubach Creek. Beaver Creek supports a rainbow trout fishery and the leaking flume could
have resulted in genetic contamination of the westslope fishery. Completed.

50. Trout Creek restoration. Trout Creek (Granite County) supports a brown trout fishery.
The stream, as it flows through the MaClain, Yardley, and Dennis ranches is channelized and has
been historically over grazed. The channelized reach, which is nearly two miles long, has
severely down cut and suffers from lateral erosion. This project involves reconstructing the
historic channel, stabilizing unchannelized reaches, revegetating stream banks and fencing and
off-stream water development to facilitate grazing management, and moving a corral away from
the stream . The entire project covers nearly 4 miles of stream. All three landowners allow
public fishing.

29

Project Descriptions - 2000

1 . Basin Creek culvert replacement. Basin Creek (Lincoln County) is a tributary to the
Kootenai River located on the Kootenai National Forest. The stream supports a native
population of red band trout - a species of special concern. The purpose of the project is
to provide fish passage and to reduce sediment by replacing a culvert that is undersized
and perched. The applicants intend to use this project as an example and incentive for the
US Forest Service to replace similar culverts in the drainage.

2. Upper Big Hole off-stream water. The upper Big Hole River (Beaverhead County)
supports the last remaining population of fluvial arctic grayling in the lower 48 states.
Unfortunately, the upper Big Hole is dewatered during low flow years. This project
supplements ongoing efforts to improve stream flow in the upper river by providing off-
stream watering for cattle thereby reducing the need to divert water. This project
involves several improvements to the existing watering system making it more workable.

3. Bitterroot River riparian fence. The Bitterroot River (Missoula County) south of
Missoula is one of Montana's premier trout streams. This project will involve installation
of 1.2 miles of riparian fencing to prevent impacts due to grazing. A grazing management
plan is required.

4. Bynum Reservoir spawning habitat. Bynum Reservoir supports popular fisheries
for yellow perch and walleye. Several different types of structures were installed during
a previous project; these were monitored by divers to evaluate their suitability as
spawning substrates for yellow perch. This project involved installation of additional
Scotch pine spawning structures - Scotch pine were the most heavily used during
previous installations. Completed.

5. Canyon Creek riparian fence. Canyon Creek (Lewis and Clark County) on the
Grady Ranch was the site of a previous stream restoration project. This project involved
construction of riparian fencing along approximately 0.5 miles of Canyon Creek (and a
small tributary) to provide more controlled grazing management. Completed.

6. Cottonwood Creek channel restoration. Cottonwood Creek (Fergus County) is an
important trout stream located about 8 miles southwest of Lewistown. A reach of
Cottonwood Creek located on the Floyd Maxwell ranch is severely incised and suffers
from steep, raw, eroding banks. This project involves creating 2,700 ft of newly restored
channel and moving the stream to the new channel - allowing it to regain access to its
floodplain.

7. Cottonwood Creek fish barrier. Cottonwood Creek (Choteau County), located on
the Lewis and Clark National Forest, supports a genetically pure population of westslope
cutthroat trout. The project involves installation of a barrier to protect the genetic purity
of the population.

30

8. Dry Creek riparian fencing. Dry Creek (Broadwater County) is an important
spawning stream for rainbow trout from the Missouri River. This project involves
installation of fencing on both sides of about 4,700 ft of stream. Grazing will be
managed in streamside areas to promote regeneration of woody vegetation.

9. Dupuyer Creek channel restoration. Dupuyer Creek (Pondera County) supports a
resident population of rainbow trout. This project included returning the stream to an old
meander channel to increase stream length and improve fish habitat and bank stability.
Treatments included root wads, bank shaping, and willow plantings; approximately 1800
ft of channel was restored. Completed.

10. East Fork Bull River channel restoration. East Fork of the Bull River (Sanders
County) supports populations of both westslope cutthroat trout and bull trout. This
project involves restoring approximately 1.200 ft of stream by returning a braided
channel to a single thread channel that is capable of transporting sediment and conveying
bankfull flows. Treatments include rootwad and log revetments, placement of large
woody debris weirs, and revegetation of stream banks and the floodplain with native
shrubs and tree seedlings.

1 1 . Flatwillow Creek riparian fencing. Flatwillow Creek (Fergus County) supports a
popular local fishery for brown and brook trout. The applicant proposed to fence 3.500 ft
of stream to protect a reach that will be restored. However, the project was cancelled
when ownership of the property changed. Cancelled.

12. Flint Creek off-site water and riparian fencing. Flint Creek (Granite County)
supports a popular fishery for brown and rainbow trout. The applicant proposes to
develop a riparian grazing management plan that includes fencing and off-stream water
development. The project will improve riparian condition along approximately 3.1 miles
of stream.

13. Lost Creek headgate repair and channel restoration. Lost Creek (Deer Lodge
County), a tributary to the upper Clark Fork River, supports populations of both brown
and rainbow trout. This project involves reconstructing an old irrigation diversion in a
manner that will prevent the ditch from capturing the entire flow of the stream and
restoring and protecting the old abandoned stream channel. Approximately 3.6 miles of
stream will be restored.

14. McCabe irrigation efficiency. McCabe Creek (Powell County), a tributary to
Monture Creek, supports a population of genetically pure westslope cutthroat trout. The
stream suffers from seasonal dewatering due to a series of irrigation diversions; fish are
also lost down the ditches. Additionally, one reach of the stream is channelized and has
very little usable habitat. This project involves consolidating the diversions, installing a
fish screen as well as a more efficient irrigation system that will allow salvaged water to
be left instream. The channelized reach will be returned to its historic channel and
woody debris will be added to improve channel diversity.

31

15. North Fork Burnt Creek riparian fencing. North Fork Burnt Creek (Ravalli
County), a tributary to the Bitterroot River near the Lee Metcalf Wildlife Refuge,
supports a mixed trout population. This project involves installing 7,400 ft of riparian
fencing.

16. Prickly Pear channel restoration. Prickly Pear Creek (Lewis and Clark County)
located in the Helena valley supports a mixed trout fishery. The reach that flows through
the Burnam Ranch suffers from a variety of problems caused by adjacent land
management practices. The owner is in the process of entering into a CRP agreement
with the NRCS that will result in cattle being excluded from streamside areas for a
minimum of 10 years to allow riparian areas to recover. This project will further the
recovery and includes installation of riparian fencing and native material revetments,
revegetation of selected areas with willow clumps, and re-alignment and narrowing of
portions of the channel to facilitate sediment transport and improve fish habitat.
Approximately 2,100 ft of stream will be treated.

17. Prospect Creek channel restoration. Prospect Creek (Sanders County) supports a
mixed trout population that includes both bull and westslope cutthroat trout. The stream
has become degraded from a variety of activities including road building, pipeline
construction, and various land use activities that resulted in removal of riparian
vegetation. Portions of the stream have already undergone restoration work. This project
involves restoring selected reaches along an additional 1 1 miles of stream. Treatments
will include channel shaping to establish a more favorable width/depth ratio, intensive
revegetation of the floodplain, and native material revetments.

18. Racetrack Creek off-site water and riparian fence. Racetrack Creek (Powell
County) is an important spawning stream for Clark Fork River brown trout. The stream in
the project reach is degraded primarily due to grazing. This project involves riparian
fencing, off-stream water development and revegetation along approximately 1.2 miles of
stream.

19. Ruby Creek flow enhancement. Ruby Creek/North Fork Big Hole River
(Beaverhead County) is a critical area for fluvial arctic grayling. There has been an
ongoing effort to provide off-stream watering thereby eliminating the need to divert water
for stock. This project was a continuation of this effort and involved installation of a
well, pipeline, and two watering tanks. Completed.

20. South Fork Musselshell River fish passage. South Fork Musselshell River near
Martinsdale supports a resident population of brown trout. This project involves

modifying an existing irrigation diversion to allow fish passage. This will open up
several miles of the upper South Fork to spawning.

21. South Fork Willow Creek bank stabilization and riparian fencing. South Fork
Willow Creek near Harrison (Madison County) supports resident populations of

32

Brown, brook, and rainbow trout. This project involves backsloping, revegetation and
installation of log veins, root wads, and riparian fencing to improve bank stability and
promote recovery of woody vegetation. Car bodies and other trash will also be removed
from streamside areas and off-stream water will be developed. Approximately 1.25 miles
of stream would be treated.

22. Stillwater River side-channel restoration. Stillwater River (Stillwater County)
supports a resident rainbow trout population. This project involved developing an
abandoned side channel to serve as a spawning channel. Gated culverts were installed in
an existing inlet channel plug to control flow. Pools were developed and gravel was
added to riffles for spawning. Completed.

23. Sun River channel restoration. Sun River (Cascade County) supports resident
populations of brown and rainbow trout. The stream in the area of an old gravel mining
operation is extremely wide, shallow, and braided - very little fish habitat is present.
This project will return the stream to a more natural and stable pattern and promote
sediment transport. Banks will be stabilized using root wad revetments and rock veins
and boulders will be used to establish a grade control. Additionally, the river will be
diverted through a re-constructed side channel to regain additional channel length.

24. Sweathouse Creek fish screen. Sweathouse Creek (Ravalli County) on the Leslie
Hinman property supports a resident population of brook trout. This project involves
replacing an existing headgate with a turbulent fountain screen. This new system will
prevent fish from being lost down the ditch.

25. Tenmile Creek riparian restoration. Tenmile Creek (Lewis and Clark County)
supports a mixed resident trout population. The stream is degraded due to reading and

adjacent land use practices. A local watershed group initiated a riparian revegetation
project last year that was partially funded with Future Fisheries dollars. This project was
a continuation of the riparian revegetation effort. Completed.

26. Trail Creek fish ladder and screen. Trail Creek (Missoula County) supports a
mixed trout fishery that includes bull and cutthroat trout. A proposal to restore an old
irrigation diversion will create a barrier to fish migration. This project involves installing
a fish ladder and a non-mechanical screen on the irrigation diversion.

27. Virginia Creek channel restoration. Virginia Creek (Lewis and Clark County)
supports a mixed resident trout population. Instream ponds and dams have degraded the
stream as it flows through a series of private lots. This project would have involved
removing a small concrete dam to drain a pond and reseeding and revegetating
streamside areas. Approximately 270 ft of stream would have been treated. Cancelled.

28. Warren Creek channel restoration. Warren Creek (Powell County) supports a
mixed trout assemblage including brown, rainbow, cutthroat, and bull trout. The stream is
degraded due to previous channelization and grazing. This project involves restoring

33

9,200 ft of stream. Treatments include rebuilding and restoring stream length in the
channelized reach, rebuilding the flood plain, back-sloping and revegetating vertical
eroding banks, and placement of woody debris in the channel to improve fish habitat.

29. West Fork Wilson Creek fish barrier. West Fork Wilson Creek (Gallatin County),
a tributary to the West Gallatin River, supports a genetically pure population of westslope
cutthroat trout. An irrigation diversion in the lower reach of the stream has effectively
prevented ingress of non-native species and subsequent hybridization. Unfortunately, the
existing diversion is about to fail. This project involves replacing the existing barrier
with a more permanent structure

30. Yellowstone River riparian demonstration. Banks of the Yellowstone River (Park
County) south of Livingston have been treated with many miles of rip-rap and rock barbs
in recent years because of the fear of property damage caused by flooding. The purpose
of this project is to serve as a demonstration of softer, more natural methods of stabilizing
banks using shrubs and trees. Approximately 0.6 miles of bank will be treated.

31. Big Creek fish screen. Big Creek (Ravalli County), a tributary to the Bitterroot
River near Stevensville, supports a mixed assemblage of trout including spawning runs
from the Bitterroot. The ditch presently traps migrating fish. The Big Creek Ditch
Company is in the process of reconstructing the headgate and diversion. This project
involves retrofitting the new diversion structure with a self-cleaning fish screen.

32. Bitterroot River fish screen. The Republic Canal which diverts water from the
Bitterroot River near Hamilton (Ravalli County) entraps large numbers offish from the
Bitterroot each year. Sleeping Child Creek enters the river just upstream of the ditch
diversion and is a spawning stream for the Bitterroot; juvenile fish entering the Bitterroot
are likely lost down the ditch. This project involves installation of an overflow crest
screen on the diversion to prevent fish from entering the ditch.

33. Butler Creek fish passage. Butler Creek (Missoula County) supports a genetically
pure population of westslope cutthroat trout. Three structures (a rock sill, an undersized
culvert, and an old irrigation diversion) presently obstruct fish passage and fragment
habitat in Butler Creek. This project involves eliminating all three of these barriers.

34. Canyon Ferry perch spawning habitat structures. Canyon Ferry Reservoir
(Broadwater and Lewis and Clark counties) supports a popular yellow perch fishery. The
Helena Chapter of Walleye Unlimited and FWP have worked together to install yellow
perch spawning and rearing structures constructed from Christmas trees; this project is an
expansion of previous efforts.

35. Dempsey Creek corral relocation. Dempsey Creek (Powell County), a tributary to
the Clark Fork River located south of Deer Lodge, supports genetically pure westslope
cutthroat trout and brook trout. This project involves removing a streamside corral

34

and restoring riparian vegetation. Off-stream watering will also be developed.
Approximately 1,200 ft of stream will benefit.

36. Kolb Spring Creek restoration and fencing. Kolb Spring Creek (Missoula County)
which enters the Bitterroot River near Lola supports a mixed assemblage of trout and has
great potential as a spawning and rearing stream. The creek has been channelized and has
become entrenched over most of its length. This project involves reconstructing and
restoring approximately 5,500 ft of stream.

37. Newian Creek riparian fencing. Newlan Creek (Meagher County), which flows out
of Newlan Creek Reservoir near White Sulphur Springs, supports a mixed trout
population. The project area has minor impacts due to livestock grazing. This project
would have involved riparian fencing. Cancelled.

38. O'Brien Creek riparian fencing. O'Brien Creek (Missoula County) supports a
population of westslope cutthroat as well as other trout species. Bitterroot River fishes
also use O'Brien Creek for spawning. Riparian areas in the project reach are degraded
due to grazing and brush removal. This project involves installing riparian fencing along
both sides of 400' of stream and complements other projects that have recently been
completed.

39. Poorman Creek channel restoration. Poorman Creek (Lewis and Clark County),
which enters the Blackfoot River near Lincoln, supports a mixed salmonid population
that includes westslope cutthroat. The stream was historically placer mined and has been
more recently manipulated by road building and landowners living along the creek. This
project involves restoring approximately 700' of stream using a variety of treatments as
well as replacing an undersized culvert with a bridge.

40. Silver Butte/Fisher Creek bank stabilization. Silver Butte/Fisher River (Lincoln
County) supports cutthroat trout and some bull trout. The stream is unstable in the
project area due to past grazing and land use. This project involves stabilizing the bank
using rock vanes, J-hook weirs, and rootwads. Riparian fencing will also be installed.

41. Tongue River riparian fencing. The Tongue River (Rosebud County) is one of the
most important streams in southeastern Montana. In the project area, the stream supports
sauger, channel catfish, walleye, and smallmouth bass. Streambanks in the project area
have been damaged by previous grazing practices. This project involves construction of
two miles of riparian fencing and installation of two water gaps. Streamside areas will be
managed to promote recovery of woody riparian vegetation.

42. Trout Creek fish ladder. Trout Creek (Lewis and Clark County) flows into Hauser
Reservoir east of York. The stream supports a mixed salmonid population that includes
spawning trout and salmon from Hauser Reservoir. An irrigation diversion located about
2 miles upstream from York is presently a barrier to fish migration. This project involves
retrofitting the diversion with a Denil fish ladder that will open up about 6.8 miles of
stream for spawning.

35

43. Wolf Creek fish passage. Wolf Creek (Lewis and Clark County) enters Little
Prickly Pear Creek near the town of Wolf Creek. Little Prickly Pear and its tributaries
support the most important spawning run of trout from the blue ribbon reach of the
Missouri located below Holter Dam. A diversion on Wolf Creek is presently a barrier to
fish migration. Nearly 300 rainbow trout spawners were found pooled up below the dam
during spring 2000. This project involves creating a series of step-pools below the
diversion that will allow migrating fish to move upstream.

44. Northeast Montana pond aeration. Fishing ponds in North-central Montana
commonly winterkill due to oxygen depletion. Many of these ponds are capable of
maintaining self-sustaining fisheries, primarily bass and yellow perch, were it not for the
oxygen problem. This project involved installation of wind powered aeration pumps on 8
ponds to maintain oxygen levels over the winter and allow naturally reproducing fish
populations to sustain themselves. Completed.

36

Appendix A

Future Fisheries Improvement Program
Monitoring Report - 2000

by

Bradley B. Shepard

Montana Department of Fish, Wildlife and Parks

Montana Cooperative Fishery Research Unit

Biology Department, MSU

Bozeman, Montana 59717-0001

December 2000

Table of Contents

Table of Contents »

List of Tables ii'

List of Figures 1U

Introduction 1

Beaverhead River Drainage 1

Stone Creek Rehabilitation 1

Big Hole River Drainage 2

Deep Creek Channel Restoration 2

Bitterroot River Drainage 3

Camp Creek Channel Restoration 3

Blackfoot River Drainage 4

Bear Creek Channel Reconstruction 4

Blanchard Creek Fish Passage, Riparian Fencing, and Feedlot Removal 5

Chamberlain Creek Fish Passage and Irrigation Diversion 7

Cottonwood Creek Fish Friendly Diversion, Dryer Diversion Lining, and Fish Screen

Improvement °

Gilbert Creek Irrigation Diversion Screen and Fish Passage 9

Gold Creek Pool Development 10

Kleinschmidt Creek Channel Restoration, Phase II 1 1

McCabe Creek Barrier Removal, Debris Placement, Culvert Replacement 13

Monture Creek Stream Restoration 14

Pearson Creek Woody Debris Placement 16

Rock Creek Restoration, Dry Creek Restoration, and Burmit Project 16

Boulder River Drainage 18

Muskrat Creek Migration Barrier 18

Clark's Fork River Drainage 19

East Fork Bull River Bank Stabilization and Channel Restoration 19

Elk Creek Channel Restoration 20

Prospect Creek Channel Restoration 21

Rock Creek (Garrison) Instream Flow and Habitat Improvement Project Channel 21

Jefferson River Drainage 22

Hell's Canyon Creek Irrigation Modification 22

South Willow Creek Bank Stabilization 23

Judith River Drainage 25

Big Springs Creek Brewery Flats Channel Restoration 25

Cottonwood Creek Channel Restoration 26

Missouri River Drainage 28

Canyon Ferry Yellow Perch Habitat Enhancement 28

Highwood Creek Channel Rehabilitation 29

Magpie Creek Fish Passage 32

Missouri River Bank Stabilization - Range and Below Craig 32

Missouri River Big Springs Spawning Channel 34

White's Gulch Rehabilitation and Barrier 35

Musselshell River 37

Page A-ii
December 2000

South Fork Musselshell Irrigation Diversion Fish Passage 37

Sun River Drainage 38

Spring Coulee Bank Stabilization 38

Sun River Inventory and Design - Simms to Fort Shaw; Bank Stabilization 42

Yellowstone River Drainage 42

Big Creek Irrigation Efficiency 42

Mol Heron Creek Flow Enhancement and Fish Screen 44

Stillwater River Channel Restoration 44

Acknowledgements 45

References 45

List of Tables

Table 1. Number of brown and rainbow trout redds observed in the Big Springs spawning

channel of the Missouri River from 1994 to 1999 35

List of Figures

Figure 1. Relative abundance (catch in a single electrofishing pass per 1,000 feet of channel) of
grayling, brown trout, rainbow trout, brook trout, ling, mountain whitefish, and
suckers in restored (Treatment: T) and Control (Untreated: C) sections of Deep Creek
in 1998 and 1999 3

Figure 2. Estimated populations and 95% confidence intervals (vertical lines; 95% CI) of all
species combined (cross-hatched bars) 4.0 inches and longer per 1,000 feet of stream
length and species composition (westslope cutthroat - WCT, rainbow, brown, brook,
and bull trout) in Bear Creek at stream miles 1.1 and 1.5 from 1998, prior to channel
restoration, through 2000 5

Figure 3. Estimated population of rainbow trout < 4.0 inches and 4.0 inches and longer at
Stream Mile 0.1 in Blanchard Creek from 1990 to 1999 standardized to estimated
number per 1 ,000 feet of stream length. Vertical bars represent 95% confidence
intervals (95% CI) 6

Figure 4. Relative abundance (catch in a single electrofishing pass per 1,000 feet of stream
length) of westslope cutthroat (WCT), rainbow (RB), and brown trout in a sample
section located at stream mile 0.1 in Chamberlain Creek from 1989 to 2000. It should
be noted that 1989 data was collected in a portion of stream that had been recently
modified by a bulldozer 7

Figure 5. Relative abundance (catch in a single electrofishing pass per 1,000 feet of stream

channel) for westslope cutthroat (WCT), bull, and brook trout 4.0 inches and longer in
a sample section of Cottonwood Creek located at stream mile 12.0 from 1997 to
2000 9

Figure 6. Relative abundance (catch in a single electrofishing pass per 1 ,000 feet of stream

channel) for westslope cutthroat (WCT), bull, rainbow (RB), brown, and brook trout
4.0 inches and longer in a sample section of Gilbert Creek located at stream mile 2.0
from 1995 to 2000 10

Page A-iii
December 2000

Figure 7. Relative abundance (catch in a single electrofishing pass per 1,000 feet of stream
length) of westslope cutthroat (WCT), bull, rainbow (RB), and brown trout in a
sample section located at mile 1.9 in Gold Creek from 1996 to 2000 1 1

Figure 8. Relative abundance (catch in a single electrofishing pass per 1 ,000 feet of stream

channel) for young-of-the-year (YOY) and age 1 and older (1+) brown and brook trout
in a sample section of Kleinschmidt Creek located at stream mile 0.8 from 1998 to
2000 12

Figure 9. Relative abundance (catch in one electrofishing pass per 1 ,000 feet of stream channel)
of westslope cutthroat (WCT) and brook trout estimated in two sample sections of
McCabe Creek in 1999 and 2000 14

Figure 10. Counts of bull trout redds (spawning sites) in Monture Creek from 1989 to 2000. ..15

Figure 1 1 . Relative abundance (catch in one electrofishing pass per 1 ,000 feet of stream length)
of young-of-the-year (top) and age 1 and older (bottom) rainbow, brown, and brook
trout in two sections (mile 0.7 and 1.7) of Rock Creek from 1990 to 2000 17

Figure 12. Number of westslope cutthroat (WCT), brown, brook, and bull trout estimated per
1,000 feet of channel length (standard deviations shown by vertical lines) in the
proposed FFI project area (Treatment) and a control area upstream during 2000 19

Figure 13. Number of trout (westslope cutthroat and brook trout combined) estimated for five
sections of Elk Creek in 1997 (pre-project) and from 1998 to 2000 (post-project).
Estimates were made in two bank stabilization treatment sections (BS1 and BS2), two
sections where the channel was reconstructed (New 1 and New 2), and one control
section in a Wilderness Area (Control) 20

Figure 14. Numbers of bull (BT) and westslope cutthroat trout (WCT) estimated per 1,000 feet
of stream length by stream mile in 1999 and 2000. The FFI channel restoration
projects were located at mile. 17 22

Figure 1 5. Length frequency histograms for brown trout (left) and rainbow trout (right) captured
in an upper Control Section (top) and lower FFI Section (bottom) of South Willow
Creek in 2000 24

Figure 16. Estimated number and standard deviations (vertical lines) of brown trout (left) and
rainbow trout (right) 6.0 inches and longer in both a section where FFI funds will be
spent on bank stabilization (FFI Section) and in an upper Control Section of South
Willow Creek during 2000 24

Figure 17. Estimated number and 95% confidence intervals (vertical lines) of rainbow trout 10
inches and longer per mile in three sections of Big Springs Creek from 1967 to 2000.
26

Figure 18. Estimated numbers (standard deviations shown as vertical capped lines) of brook

trout (standardized to number per 1,000 feet of stream channel) 6.0 inches and longer
in a FFI habitat restoration section and Control section of Cottonwood Creek in 2000.
27

Figure 19. Length frequencies for brook trout captured in the FFI Section (cross hatch bars) and
a Control Section (grid bars) of Cottonwood Creek in 2000 28

Figure 20. Numbers (standard deviations shown as vertical capped lines) of brown trout,
rainbow trout, and brook trout (standardized to number per 1 ,000 feet of stream
channel) 6.0 inches and longer estimated for a FFI habitat restoration section and
Control section of Highwood Creek from 1997 to 2000 30

Page A-iv
December 2000

Figure 21. Relative catch (number offish captured on the first electrofishing pass per 1,000 feet
of channel length) for brown, rainbow, and brook trout less than 6.0 inches long in a
FFI habitat restoration section and Control section of Highwood Creek in 1999 and
2000 31

Figure 22. Length frequencies for brown trout (left), brook trout (middle), and rainbow trout

(right) captured in the FFI project area (cross hatch bars) and a control area (grid bars)
of Highwood Creek in 1999 (top) and 2000 (bottom) 31

Figure 23. Catch rates (number per 1,000 feet of river bank) for rainbow and brown trout less
than 6 inches and 6 inches and longer along six river bank sections of the Missouri
River near Craig, Montana 33

Figure 24. Relative catch (number of fish captured on the first electrofishing pass per 1 ,000 feet
of channel length) for westslope cutthroat and brook trout 3.0 inches and longer in
three areas of White's Gulch from 1993 to 2000 36

Figure 25. Relative catches (number captured in first pass per 1,000 feet) of rainbow, brown and
brook trout in three sections of Spring Coulee Creek in 1998 and 1999. Note that in
1998 warm water temperatures limited catch efficiencies in the Old and New
Treatment sections 39

Figure 26. Estimated number of brown trout (8 inches and longer), rainbow trout (11 inches and
longer) and brook trout (6 inches and longer) per 1 ,000 feet of stream length in three
sections of Spring Coulee Creek within Marc Lee's property during June 1999 40

Figure 27. Length frequencies for brook (solid bars), brown (cross-hatched bars), and rainbow
(stippled bars) trout in three sections of Spring Coulee Creek sampled in July 1998
(top) and June 1999 (bottom) 41

Figure 28. Total number (top) and catch per trap day (bottom) of Yellowstone cutthroat trout fry
captured in fry traps while emigrating from Mill, Big, Cedar, and Mol Heron creeks
from 1996 to 2000 43

Page A-v
December 2000

Introduction

This report summarizes the results of monitoring conducted from 1998 to 2000 to evaluate the
effectiveness of selected habitat restoration projects funded through the Future Fisheries
Improvement Program (FFI). Monitoring was conducted to help answer the question; "Did the
funded project improve target fish populations?" Monitoring is essential to understand what
types of projects provide benefits to fish populations and which do not. It is important to
consider that stream flows statewide were nearly normal during 1999, but were near record low
flows during 2000. The data in this report need to be viewed in this context and it was
interesting to note that while fish abundance indices for some FFI projects declined during 2000,
these indices increased or remained stable in 2000 despite these extremely low base flows.
These data suggest that for some streams extremely low flows can be partially mitigated by
improved habitat or that efforts to mitigate low flow impacts by increasing flows through FFI
efforts may be, at least, partially successful.

This report presents data collected for 53 projects. Shepard (1998) reported on fish resource
assessments for FFI Projects that had been completed through 1998. This report only summaries
information for projects where fish information was collected during the time period 1998
through 2000. These data, as well as conclusions, are considered preliminary because it often
takes five years or more for fish populations to fully respond to habitat improvement treatments
(Hunt 1976) and some of these data have not yet been fully analyzed. Of the 53 projects
evaluated in this report, baseline data is reported for 24 (45%), preliminary results were
inconclusive for 7 (13%), and preliminary data indicate fish populations are improving at 22
(42%) projects. This report is organized first by the river basin where each project is located and
then by the project name.

Beaverhead River Drainage

Stone Creek Rehabilitation

WATER NAME: Stone Creek - Beaverhead River

DATE PROVIDED BY: Dick Oswald and Brad Shepard, FWP

DETAILED REPORT CITATION: Oswald (2000)

MFWP CODE: RRA-54-1994 and FFI-16-1997

The Left Fork of Stone Creek from the Barretts Minerals, Inc. talc mine downstream (about 1.6
miles) was reclaimed from 1995 through 1997. Barretts Minerals moved most of an existing
road that had been located along the entire length of the stream away from the stream channel.
Other reclamation included rebuilding the stream channel, banks, and floodplain in several areas,
adding pools, and controlling sediment delivery to the stream channel by construction catch
basins and re-vegetating the riparian area. Populations of westslope cutthroat trout responded
relatively quickly to this restoration project within the East Fork and that response was
documented in the last report (Shepard 1998). Most recent monitoring focused on the expansion
of the westslope cutthroat trout population from the restored Left Fork area down into main
Stone Creek. Sampling soon after completion of the restoration of the Left Fork found that
westslope cutthroat had begun expanding their distribution from the Left and Middle forks down

Page A-l
December 2000

into the mainstem Stone Creek in 1998. Sampling on the mainstem found about 30 westslope
cutthroat trout per 1,000 feet in 1986, 3 in 1994, none in 1995, immediately prior to the
restoration done in the Left Fork from 1995 to 1997, and then went up to 200 per 1,000 feet in
1998, following restoration activities. Five sample sections in the mainstem from the junction of
the Left and Middle forks downstream 3.5 miles were sampled in 1995 and 1999. Sampling in
1995 found no fish in any of the sections. In 1999 westslope cutthroat trout were found in all
five sample sections and their abundance was relatively high in four of the five sections (71 to 82
fish per 1,000 feet of stream length). A section located about 2.8 miles downstream only
supported about 17 per 1,000 feet; however, the habitat in this portion of the mainstem was
severely degraded, apparently due to excessive sediment loads. Channel restoration completed
in the Left Fork not only dramatically increased the population of westslope cutthroat
trout in this stream, but led to a dramatic expansion of this population at least 3.5 miles
down the drainage.

Big Hole River Drainage

Deep Creek Channel Restoration

WATER NAME: Deep Creek - Big Hole River
DATE PROVIDED BY: Jim Magee, FWP
DETAILED REPORT CITATION: FWP files, Dillon
MFWP CODE: FFI-10-1998

A long meander loop in Deep Creek was cut off by high flows. The FFI project, completed
during June of 1998, reconnected and restored the channel in this meander loop. In October
1998 and 1999 single electrofishing passes were conducted in two 1,000 feet-long sample
sections in Deep Creek. One was located within the project area (Treatment) and another was
located in an untreated section upstream from the project area (Control). In 1999 sampling
equipment broke down while working the Control Section, consequently, no data were collected.
Catches of most fish species were similar between the Treatment and Control sections in October
1998 (Figure 1). More ling and brook trout, but fewer rainbow trout, were captured in the
Treatment Section in 1999 than in 1998. Fall sampling may not be representative of summer
use of these sections due to fall spawning migration from the Big Hole River, or movements of
non-spawners to prey on the eggs. Further sampling will be needed to determine the fish
capacity of the Treatment Section. Baseline data has been obtained, but no conclusions can
yet be reached on this project.

Page A-2
December 2000

0

o

100

«- 80 -

o
o
o

o

O

n
O

60

40 -

20

0

Grayling
Browns
K^3 Rainbow
I I Brook
f=\ Ling
m?Z\ Whitefish
17772 Suckers

Deep Creek

C(98)

T(98)
Section (Year)

T(99)

Figure 1. Relative abundance (catch in a single electro fishing pass per 1,000 feet of channel) of
grayling, brown trout, rainbow trout, brook trout, ling, mountain whitefish, and
suckers in restored (Treatment: T) and Control (Untreated: C) sections of Deep Creek
in 1998 and 1999.

Bitterroot River Drainage

Camp Creek Channel Restoration

WATER NAME: Camp Creek - Bitterroot River
DATE PROVIDED BY: Chris Clancy, FWP
DETAILED REPORT CITATION: Clancy (in prep.)
MFWP CODE: FFI-06-1999

Mark-recapture electrofishing estimates were done for brook and westslope cutthroat trout on
August 5, 1999 in a 1000-foot long section of Camp Creek located about 3.2 miles above its
mouth. The section was immediately downstream of a bridge crossing near the north end of
Section 34 (T01N;R19W; Section 27). This section is in the portion of the creek that was
channelized in the past and is slated for restoration, probably in 2001. The data collected in 1999
represents pre-project information. In 1999 this section supported an estimated 3 1 brook trout
(SD: 3.8) 4.0 to 9.0 inches in length and 379 (SD: 25.8) westslope cutthroat trout 3.0 to 14.0

Page A-3
December 2000

inches long. In addition to these species, 2 bull trout, 1 brown trout, 7 westslope cutthroat
rainbow trout hybrids, and 6 longnose suckers were also captured; however, no estimates were
made for these species. These data represent baseline data that will allow for future
evaluation of this FFI project.

Blackfoot River Drainage

Cooperative private and public fisheries restoration efforts, of which FFI program has been one
component, have been implemented within Blackfoot River drainage throughout the 1990's.
Cooperators include F WP, US Fish and Wildlife Service, US Bureau of Land Management, US
Natural Resource Conservation Service, Montana Department of Transportation, Montana
Department of Natural Resources and Conservation, North Powell Conservation District, Big
Blackfoot Chapter of Trout Unlimited, private landowners, Chutney Foundation, National Fish
and Wildlife Foundation, Montana Power Company, and Plum Creek Timber Company. Fish
evaluations for specific FFI projects often could not be separated from other cooperative projects
conducted during the same time and in the same drainages as FFI projects. Consequently, the
following evaluations should be viewed as assessments for the total effort, rather than just FFI
projects.

Bear Creek Channel Reconstruction

WATER NAME: Bear Creek - Blackfoot River

DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Pierce et al. (1997); Pierce and Schmetterling (1999);

Pierce and Podner (2000); Pierce et al. (in prep.)
MFWP CODE: FFI-28-1998

Restoration activities in Bear Creek began in 1995 using funds other than FFI funds. In 1998
FFI funds helped reconstruct 1,870 feet of channel and restore habitat in an additional 2,000 feet
of Bear Creek that had been degraded from channelization and improper logging and grazing
practices in the riparian area. This FFI project was part of a larger basin-wide collaborative
effort that included improving grazing practices, fixing under-sized culvert barriers, increasing
irrigation efficiencies, and removal of a winter livestock feed lot. In 1998 and 1999, habitat
evaluations and fish population monitoring was completed for the Bear Creek Channel
Reconstruction Project. Habitat data found that the 1,870-foot segment of restored channel
contained 62 pools, a total wetted area of 1,163 square feet, and 184 pieces of woody debris.
These data will be used to document persistence of constructed habitats through time by
repeating these habitat surveys over time. Two fish survey sections were sampled to assess the
habitat project in lower Bear Creek. Depletion estimates conducted in the restored section found
that trout over 4.0 inches increased in abundance from 126 trout per 1,000 feet of stream to 177
trout from 1 998 to 1 999; however, these increases were not significant (Figure 2). Westslope
cutthroat trout were not captured in this section in 1998, but were found in 1999. In 2000 the
first bull trout ever observed in Bear Creek was found in lower Bear Creek. The relative
abundance offish and presence of native fish appear to have initially increased following
restoration activities within the Bear Creek drainage. Baseline data on fish abundance and
habitat condition have been collected in the restored channel reach.

Page A-4
December 2000

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Figure 2. Estimated populations and 95% confidence intervals (vertical lines; 95% CI) of all
species combined (cross-hatched bars) 4.0 inches and longer per 1,000 feet of stream
length and species composition (westslope cutthroat - WCT, rainbow, brown, brook,
and bull trout) in Bear Creek at stream miles 1 .1 and 1.5 from 1998, prior to channel
restoration, through 2000.

Blanchard Creek Fish Passage, Riparian Fencing, and Feedlot Removal

WATER NAME: Blanchard Creek -Clearwater River

DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Peters (1990); Pierce et al. (1997); Pierce and

Schmetterling (1999); Pierce and Podner (2000);

Pierce et al. (in prep.)
MFWP CODE: RRA-45-94, FF1-48-96, and FFI-52-96

Blanchard Creek, a small tributary to the Clearwater River, was historically de-watered for about
a mile above its mouth by irrigation water withdrawals. Fish passage over two irrigation
diversions and the crossing under Highway 200 was very poor and probably negatively impacted
the fishery in the lower reaches of the tributary. A water lease has been in effect since 1993;
however, the water right holder began passing more flow down the lower stream channel in

Page A-5
December 2000

1991. Two diversion structures were modified in 1993 by adding fish ladders. The culvert under
Highway 200 was also modified by the Montana DOT to facilitate fish passage. In addition,
Plum Creek Timber Company and the DNRC improved management of livestock grazing within
riparian areas. Blanchard Creek supports both rainbow trout, primarily in its lower reaches, and
cutthroat trout, primarily in its upper reaches. Fish populations in lower Blanchard Creek in the
area of the diversions and water lease (stream mile 0.1) have been monitored from 1990 to 1999.
Brown and westslope cutthroat trout began inhabiting this sample section in 1992, following
increases in flows through this section. Although their densities appeared to be highly variable
between years, densities of young (< 4.0 inches) rainbow trout increased with increases in stream
flows after 1991 with the highest estimated densities occurring during 1998 and remaining high
in 1999 (Figure 3). Densities of rainbow trout dropped slightly in 2000; however, drought
conditions resulted in extremely low base flows during 2000. Rainbow trout over 4.0 inches in
length initially increased to densities over 200 per 1 ,000 feet, then declined slightly and
stabilized at densities between 100-200 per 1,000 feet. Young rainbow trout have become
more abundant in the treatment area following treatment.

Blanchard Creek - Rainbow Estimate
Stream Mile 0.1

800

Size Class (in)

Figure 3. Estimated population of rainbow trout < 4.0 inches and 4.0 inches and longer at
Stream Mile 0.1 in Blanchard Creek from 1990 to 1999 standardized to estimated
number per 1,000 feet of stream length. Vertical bars represent 95% confidence
intervals (95% CI).

Page A-6
December 2000

Chamberlain Creek Fish Passage and Irrigation Diversion

WATER NAME: Chamberlain Creek - Blackfoot River

DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Pierce et al. (1997); Schmetterling (1998; 2000); Pierce

et al. (in prep.)
MFWP CODE: FFI-09-97

The upper reaches of Chamberlain Creek support relatively high densities of cutthroat trout.
However, aquatic habitat in the lower portion of Chamberlain Creek (below Stream Mile 3.0)
was severely altered by channelization, de-watering, and poor management practices, including
livestock grazing in riparian areas and increased sediment delivery to the stream channel related
to road drainage problems. Consequently, densities of westslope cutthroat trout in this portion of
Chamberlain Creek were severely depressed. Fish passage between Chamberlain Creek and the
Blackfoot River was also inhibited by irrigation diversions. Since 1990, Chamberlain Creek has
been the focus of a comprehensive fishery restoration effort. Road drainage problems have been
fixed. Livestock management has been improved, especially around riparian areas. Water flows
have been improved through leasing agreements. Consolidating several ditches and installing a
fish ladder on the diversion that delivers water to these ditches made irrigation delivery more
efficient. Chamberlain Creek supports a significant migration of Blackfoot River fluvial
cutthroat trout with reproduction occurring in mid to upper stream reaches.

From 1989 to 2000 relative abundance offish was assessed at mile 0.1. A comparison of
electrofishing catches indicated a substantial increase in catch offish following restoration
activities and dramatic increases in abundance of westslope cutthroat trout (Figure 4). Juvenile

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2000

Figure 4. Relative abundance (catch in a single electrofishing pass per 1,000 feet of stream
length) of westslope cutthroat (WCT), rainbow (RB), and brown trout in a sample
section located at stream mile 0.1 in Chamberlain Creek from 1989 to 2000. It should
be noted that 1 989 data was collected in a portion of stream that had been recently
modified by a bulldozer.

Page A-7
December 2000

bull trout have been consistently captured in the lower 4.0 miles of Chamberlain Creek from
1997 to 2000, while sampling for a six-year period prior to 1997 captured none. These were the
first bull trout recorded in Chamberlain Creek in 1 8 years of sampling. In a radio telemetry
study where spawning westslope cutthroat trout were tagged in the Blackfoot River during 1997
and 1 998 and tracked, more radio tagged cutthroat trout moved into Chamberlain Creek to spawn
than any other Blackfoot River tributary. A few adult westslope cutthroat trout moved more than
30 miles to spawn in Chamberlain Creek. Sixty-eight westslope cutthroat redds (spawning sites)
were observed in a two mile section of Chamberlain Creek during a 1 998 redd survey. Several
spawning adult cutthroat trout were located in pools created during restoration efforts. These
adults apparently used these pools as holding sites prior to spawning. One tagged fish spawned
in the bottom end (tail-out) of one of these constructed pools. Results suggest that
rehabilitation work has led to increased spawning use of Chamberlain Creek by adult
westslope cutthroat trout from the Blackfoot River; increased catches of rearing westslope
cutthroat trout in the lower creek; and may have improved conditions in the lower creek so
that bull trout can once again use this stream for rearing, and perhaps spawning.

Cottonwood Creek Fish Friendly Diversion, Dryer Diversion Lining, and Fish Screen
Improvement

WATER NAME: Cottonwood Creek - Blackfoot River

DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Pierce and Podner (2000); Pierce et al. (in prep.)

MFWP CODE: RRA-56-94, FFI-07-96, and FFI-44-96

To help conserve native aquatic species in Cottonwood Creek several projects were undertaken.
Fish ladders were installed on two major diversions, and two irrigation canal intakes were
screened. A total 8,000 feet of irrigation canal was lined with an impermeable fabric to prevent
water loss. An estimated 8,663 acre-feet of water salvaged by lining the ditch was annually
leased for instream flow purposes. Associated with these projects were efforts to improve
riparian livestock management and negotiate conservation easements in the middle reaches of
Cottonwood Creek. Stream flow is being monitored as part of the lease effort, but is not reported
here. Past fish populations monitoring found that the previously de-watered portion of the
stream now support bull, westslope cutthroat, and brook trout, as well as, sculpins and tailed
frogs (Shepard 1998; Pierce et al. 1999). Pierce and Podner (2000) conducted fish habitat
assessments in the previously de-watered reach and a reference reach located upstream in 1999.
They found that the upstream reference reach contained four times the amount of woody debris
in the channel as the previously de-watered reach (42 versus 10 pieces per 1,000 feet of channel).
Bankfull channel widths were much wider in the previously de-watered reach than in the
reference reach (24.3 versus 19.4 feet for pools and 26.9 versus 19.0 feet for riffles). The
relative abundance of westslope cutthroat trout in a sample section located at mile 12.0 has
tripled from 1997 to 2000 (Figure 5). Prior to 1997 this segment of channel had no flow during
the low water period of late summer to early fall, as a result this section supported no fish prior
to 1997. Brook trout have increased slightly and bull trout have occassionally been captured in
this same section (Figure 5). An equipment problem in 1999 lowered capture efficiencies,
consequently the 1999 data was not included. The previously de-watered portion of
Cottonwood Creek now supports bull, brook, and westslope cutthroat trout along with
sculpins and tailed frogs. Abundance of westslope cutthroat trout in this portion of the

Page A-8
December 2000

creek appears to be increasing. Woody debris in this previously de-watered reach is less
common than an upstream reference reach and will probably take a number of years
before this previously de-watered reach recovers its potential habitat complexity in the
form of woody debris and channel features such as pools.

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Mile 12.0

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1998

1999

2000

Year

Figure 5. Relative abundance (catch in a single electro fishing pass per 1 ,000 feet of stream

channel) for westslope cutthroat (WCT), bull, and brook trout 4.0 inches and longer in
a sample section of Cottonwood Creek located at stream mile 12.0 from 1997 to 2000.

Gilbert Creek Irrigation Diversion Screen and Fish Passage
WATER NAME: Gilbert Creek - Blackfoot River
DATE PROVIDED BY: Ron Pierce, FWP
DETAILED REPORT CITATION: Pierce et al. (1997)
MFWP CODE: FFI-40-1997

Channel restoration was done for about 2.9 miles from its mouth upstream in 1996. Prior to the
project, relative fish abundance estimated at mile 2.0, within the project, by a single
electrofishing pass found only rainbow and brown trout (Figure 6). Following construction of
this project, total fish abundance increased dramatically and westslope cutthroat begin making up
an increasing proportion of the catch. Bull trout have also been occassionally observed in the
monitoring section following construction of the project. Fish abundance increased
dramatically following completion of this project.

Page A-9
December 2000

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1995

1996

1997

1998

1999

2000

2001

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Figure 6. Relative abundance (catch in a single electro fishing pass per 1 ,000 feet of stream

channel) for westslope cutthroat (WCT), bull, rainbow (RB), brown, and brook trout
4.0 inches and longer in a sample section of Gilbert Creek located at stream mile 2.0
from 1995 to 2000.

Gold Creek Pool Development

WATER NAME: Gold Creek - Blackfoot River

DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Pierce et al. (1997); Schmetterling and Pierce (1999);

Swanberg (1996); Swanberg (1997); Pierce and Podner

(2000); Schmetterling (2000)
MFWP CODE: FFI-04-96

Timber harvest of riparian conifers and the removal of large instream wood had reduced the
diversity of stream habitat in the lower three miles of Gold Creek. Prior to restoration, pool
habitats comprised less than 1% of the stream's area in this segment of Gold Creek. In 1996, a
habitat restoration project that focused on pool construction and maintenance using large woody
debris was completed. Three types of monitoring have been undertaken for the Gold Creek
Project: 1) monitoring of the habitat structures, 2) electro fishing, and 3) radio tracking of fluvial
cutthroat and bull trout. Eight months after the project was completed an estimated 50-year
flood event passed through the project area and monitoring indicated that most of the restoration
work survived this event (Schmetterling and Pierce 1999; Shepard 1998). Maximum depths of

Page A- 10
December 2000

constructed pool habitats have been monitored from 1 996 to 1 999 and while maximum pool
depths initially decreased following the filling of pools with sediments during the 1997 flood
event, maximum pool depths either stabilized or increased slightly following 1997. Swanberg
(1996 and 1997) and Schmetterling (2000) found that fluvial adult bull and westslope cutthroat
trout from the Blackfoot River use the restored area of Gold Creek seasonally during their
spawning migrations. Annual fish abundance survey results from 1 996 to 2000 have shown an
increase in fish abundance although westslope cutthroat trout declined slightly from 1998 to
2000 and brown trout declined from 1996 to 1998 before increasing dramatically in 1999 (Figure
7). Preliminary data suggest that habitat structures in confined channel types remain in
place following flood events better than structures placed in laterally extended types of
channels and treated areas in lower Gold Creek support more fish following treatment
than prior to treatment. Adult bull and westslope cutthroat trout from the Blackfoot River
are using Gold Creek seasonally as a thermal refuge and for spawning.

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Mile 1.9

1995

1996

1997

1998

Year

1999

2000

2001

Figure 7. Relative abundance (catch in a single electrofishing pass per 1,000 feet of stream
length) of westslope cutthroat (WCT), bull, rainbow (RB), and brown trout in a
sample section located at mile 1 .9 in Gold Creek from 1996 to 2000.

Kleinschmidt Creek Channel Restoration, Phase II

WATER NAME: Kleinschmidt Creek - Blackfoot River

DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Pierce (1991); Pierce et al. (1997); Pierce and

Schmetterling (1999); Pierce and Podner (2000)
MFWP CODE: FFI-14-1998

Page A- 11
December 2000

Kleinschmidt Creek, a spring creek to the North Fork Blackfoot River, has been severely
degraded by past channel straightening and improper livestock grazing. Whirling disease is
present in this stream. Approximately 2,500 feet of channel have been restored through a
previous channel restoration project. Phase II will restore the remaining 5,300 feet of channel in
the near future. Four types of monitoring are included in this project: 1) pre- and post project
habitat surveys, 2) fishery response to habitat restoration, and 3) temperature studies, and 4) pre-
and post-project whirling disease evaluations (sentinel fish cage studies plus macroinvertebrate
including Tubifex tubifex sampling). Fish population survey, thermograph, and whirling disease
results are reported. Fish abundance surveys were done in 1 998 and 1 999 at two locations
(stream mile 0.5 and 0.8) and in 1999 at another reference location at mile 1.1. The survey at
mile 0.5 was located in the degraded section of channel slated for restoration in 2000. The
survey at mile 0.8 was completed in a section of channel restored in 1997 and the survey at mile
1.1 is a control section. Fish abundance of age 1 and older brook and brown trout increased from
1998 to 2000 in both of the lower two sections; however, increases were higher for restored
portion of the channel (Figure 8). Brook trout were more abundant than brown trout in the mile

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Mile 0.8

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Fish Age (Sample Year)

Figure 8. Relative abundance (catch in a single electro fishing pass per 1 ,000 feet of stream

channel) for young-of-the-year (YOY) and age 1 and older (1+) brown and brook trout
in a sample section of Kleinschmidt Creek located at stream mile 0.8 from 1998 to
2000.

1 . 1 Section and the first bull trout documented within the Kleinschmidt drainage in recent years
was also found in this upper section. Water temperatures during the summer of 1 999 warmed 2-

PageA-12
December 2000

3 degrees F from the restored segment at mile 0.8 down to the untreated degraded section below
mile 0.5. Whirling disease was assessed using fish in sentinel cages place in lower Kleinschmidt
Creek in 1998 and 1999 and increased from a 2.8 to a 3.6 infection grade from 1998 to 1999.
Most of the sentinel fish in 1999 suffered from grade 3 and grade 4 infection levels that could
potentially cause population impacts (Vincent 1999). Preliminary data indicated that fish
abundance in the portion of Kleinschmidt Creek increased in response to a channel
restoration treatment compared to a lower untreated section. Water temperatures appear
to warm through the untreated, degraded section in the lower stream that is slated for
restoration. Whirling disease will likely impact those fish species susceptible to it in the
stream, and the lack of rainbow trout in the stream is interesting and may result from a
synergistic effect of both disease and poor quality habitat.

McCabe Creek Barrier Removal, Debris Placement, Culvert Replacement

WATER NAME: McCabe Creek - Blackfoot River

DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Pierce and Podner (2000)

MFWP CODE: FFI-38-97; FFI-31-1998

McCabe Creek has had a long history of channel alteration and improper land management
activities that have adversely impacted fish populations including poorly designed road crossing
and irrigation diversions, improper riparian grazing practices, and physical channel alterations.
In 1999 a major restoration project was undertaken in McCabe Creek to: 1) consolidate four
separate irrigation ditches into a single pipeline and screen the intake; 2) convert from flood to
sprinkler irrigation to increase water efficiency; 3) place woody debris in the channel and plant
shrubs along 0.5 mile of stream channel; 4) alter riparian livestock grazing practices to be more
compatible for protecting riparian habitats; and 5) replace a poorly designed culvert at a county
road crossing. In 1999 fish population survey sites were established at stream mile 2.3, below
the lowermost irrigation diversion in an area that had been de-watered and damaged from
improper livestock grazing, and at mile 3.2, above most management impacts where stream and
riparian habitat was in relatively good condition. In late 1 999, an irrigation ditch was screened
near mile 3.2 and base streamflows approximately doubled due to increased irrigation efficiency.
The relative catch of westslope cutthroat trout in a single electrofishing pass was much lower at
mile 2.3 than at mile 3.2 in 1999, prior to project construction (Figure 9). Following
construction, abundance of brook trout increased at mile 2.3. No brook trout were captured at
mile 3.2, while 5 per 1 ,000 feet were captured at mile 2.3. Baseline fish abundance data has
been collected to evaluate FFI projects in McCabe Creek and these data indicate that
degraded portions of the stream slated for restoration had much lower abundance of
westslope cutthroat trout than portions of the stream in relatively good condition and
westslope cutthroat trout abundance increased in 2000 following restoration activities, in
spite of drought conditions.

Page A- 13
December 2000

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Figure 9. Relative abundance (catch in one electrofishing pass per 1,000 feet of stream channel)
of westslope cutthroat (WCT) and brook trout estimated in two sample sections of
McCabe Creek in 1999 and 2000.

Monture Creek Stream Restoration

WATER NAME: Monture Creek - Blackfoot River

DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Pierce et al. (1997); Pierce and Schmetterling (1999);

Pierce and Podner (2000)
MFWPCODE: FFI-12-1997; FFI-49-1999

Monture Creek, a large tributary to the middle Blackfoot River, is an important spawning stream
used by fluvial bull and cutthroat trout inhabiting the lower Blackfoot River. From 1991 to
1998, improvements have been made in riparian livestock management along 9.3 miles (about
80%) of the mainstem of Monture Creek. In 1997 a cooperative stream restoration project
placed large woody debris in two sections of stream, totaling 1 7,606 feet of channel. Extensive
restoration work and improved riparian livestock management have been done in many of the
tributaries to Monture Creek. In addition, fishing regulation changes that went into effect in
1990 have led to increases in bull trout. Three types of information were collected to monitor
these projects: 1 ) woody debris frequency: 2) bull trout redd counts; and 3) estimating abundance
of juvenile bull trout in five long-term sample sites. Woody debris frequency surveys were
reported in Shepard (1998). Redd (spawning site) counts have shown that bull trout are
responding to habitat restoration measures in Monture Creek. Numbers of bull trout redds

Page A- 14
December 2000

steadily increased from 1989 to 1997 and then leveled off slightly before rising again in 1999
and 2000 (Figure 10).

The relative abundance of juvenile bull trout has also increased dramatically from 1989 to 2000
in five sections throughout Monture Creek from its mouth upstream 12 miles. The total catch
(summed over several sections) per 1,000 feet has increased from 7 to 66 juveniles from 1989 to
1998 before dropping slightly to 41 per 1,000 feet in 2000. The lower numbers observed in 2000
were probably related to drought effects. Increased spawning and juvenile bull trout in Monture
and other Blackfoot River tributaries, most notably the North Fork, have led to increased
abundance of sub-adult and adult bull trout in the main Blackfoot River (Pierce et al. in prep.).
Preliminary data suggest that bull trout use of Monture Creek is increasing. While the
exact cause of this increase is not yet proven, the restoration of the lower creek has
probably contributed to this increase.

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Bull Trout Redds

o

1988 1990 1992 1994 1996 1998 2000

Year

Figure 10. Counts of bull trout redds (spawning sites) in Monture Creek from 1989 to 2000.

Page A- 15
December 2000

Pearson Creek Woody Debris Placement
WATER NAME: Pearson Creek- Blackfoot River
DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Pierce and Podner (2000); Schmetterling (2000)
MFWPCODE: FFI-52-1999

Pearson Creek is a small second order tributary to Chamberlain Creek that has had a history of
channel alterations, irrigation de-watering, and improper land management impacts along its
lower 2 miles. Between 1999 and 2000 instream habitat restoration, fencing of the riparian area
along with off-channel water developments, and shrub plantings along the streambanks were
completed. Single electrofishing passes were conducted at stream mile 1.1 in 1999, prior to
restoration work, and in 2000, following restoration work. Relative catches of westslope
cutthroat trout young-of-the-year were similar between the two years (277 versus 260 per 1,000
feet of stream in 1999 and 2000, respectively), but abundance of age 1 and older westslope
cutthroat trout increased dramatically between 1999 and 2000 (42 versus 277). Abundance of
age 1 and older westslope cutthroat increased immediately following restoration work;
however, it is too early to attribute this increase solely to the FFI project.

Rock Creek Restoration, Dry Creek Restoration, and Rock Creek Restoration, Burmit
Project

WATER NAME: Rock Creek - Blackfoot River

DATE PROVIDED BY: Ron Pierce, FWP

DETAILED REPORT CITATION: Peters (1990), Pierce (1991), Pierce et al. (1997), Pierce

and Schmetterling (1999), Koopal (1998); Pierce and

Podner (2000)
MFWP CODE: FFI-05-1996, FFI-33-1996, and FFI-18-1998

Rock Creek, an 8.2 mile tributary to the lower North Fork of the Blackfoot River, has been the
focus of extensive restoration efforts, with projects completed on 5.5 miles of stream. In 1999
monitoring focused on the evaluating the newly restored 2,507 feet of channel. Monitoring done
from 1998 to 2000 included: 1) habitat surveys, 2) temperature monitoring, and 3) fish
population monitoring at two locations. Habitat surveys were completed in both 1998 and 1999
for the newly restored channel and found that this segment of channel had increased in length
167% (from 2,507 to 4,193 feet) and wetted widths had decreased from 22.5 feet to 8.5 feet. In
addition, the amount of instream woody debris increased from none to 92 pieces per 1 ,000 feet of
channel. Fish abundance data suggested that abundance of both young-of-the-year and age 1 and
older brook and brown trout at mile 1.7 declined from 1998 to 1999, before increasing
dramatically in 2000 (Figure 11). Preliminary data suggest that habitat restoration in Rock
Creek has increased woody debris frequencies, increased channel length by 167%, and
decreased channel width; however, it will probably take a few years before fish abundance
responds.

Page A- 16
December 2000

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Rock Creek - Age 1 and older
Miles 0.7 and 1.7

0.7(90) 0.7(94) 0.7(98)

1.7(98) 1.7(99) 1.7(00)

Mile (Year)

Figure 1 1 . Relative abundance (catch in one electro fishing pass per 1 ,000 feet of stream length)
of young-of-the-year (top) and age 1 and older (bottom) rainbow, brown, and brook
trout in two sections (mile 0.7 and 1.7) of Rock Creek from 1990 to 2000.

Page A- 17
December 2000

Boulder River Drainage

Muskrat Creek Migration Barrier

WATER NAME: Muskrat Creek - Boulder River
DATE PROVIDED BY: Brad Shepard and Ron Spoon, FWP
DETAILED REPORT CITATION: Shepard and Spoon (in prep.)
MFWPCODE: FFI-56-1997

Muskrat Creek supports a genetically pure population of westslope cutthroat trout. FWP, in
cooperation with USDI Bureau of Land Management and the USDA Forest Service, have been
recovering the existing population of westslope cutthroat trout in Muskrat Creek. This effort has
involved: 1) construction of a barrier near the Forest boundary (about stream mile 6.5); 2)
capturing westslope cutthroat trout from the portion of creek between this constructed barrier and
a natural barrier located at approximately stream mile 8.0 (above which the stream was Ashless)
and moving captured westslope cutthroat trout above this natural barrier; and 3) capturing brook
trout between the constructed and natural barrier and moving them below the constructed barrier.
FFI funds were used in construction of the permanent barrier to upstream fish movement near the
Forest Service boundary to prevent brook trout from moving upstream into the portion of the
creek occupied by westslope cutthroat trout. From 1997 to 2000 brook trout from the lower
portion of the creek (permanent constructed barrier to the natural barrier) were moved down
below the constructed barrier. In 1997 we moved 48 westslope cutthroat trout above the natural
barrier and almost 1 ,900 brook trout below the constructed barrier. In 1 998 we moved another
99 westslope cutthroat trout above the natural barrier and transported almost 1,500 brook trout
below the constructed barrier. In 1 999 and 2000 we did not move any additional westslope
cutthroat trout upstream, but did move 1 ,000 and 976 brook trout, respectively, below the
constructed barrier. Those brook trout transported below the constructed barrier from 1 998 to
2000 had their adipose fin removed so we could assess whether they were able to migrate back
upstream over the constructed barrier. Unfortunately, in 1998 and 1999 we held brook trout that
had been adipose clipped in a holding pen near the mouth of Nursery Creek (above the
constructed barrier) prior to transporting them below the constructed barrier. We are reasonably
sure that a few of these adipose fin-clipped brook trout, especially those under 100 mm, escaped
from this holding pen. In addition, we know of at least one adipose fin-clipped adult brook trout
that was accidentally released back into Muskrat Creek in 1999 immediately after it was clipped.
To date, we have recaptured one adipose fin-clipped brook trout above the constructed barrier in
1999 (7.0 inches in length) and three in 2000 (lengths of 4.6, 7.1, and 7.4 inches). Sampling
below the constructed barrier in 1 999 and 2000 found many adipose fin-clipped brook trout
present below the barrier. At this point, we believe that no brook trout have successfully moved
upstream past the constructed barrier due to the very small number of recaptures we have seen
above the barrier and the probability that some fin-clipped fish escaped into the stream above the
barrier when processed. Initial observations at the constructed fish barrier and recapture
rates above the constructed barrier indicate that brook trout cannot pass over the barrier;
however, we will need to totally remove brook trout from above the barrier before we can
ascertain with certainty that the barrier is effective.

Page A- 18
December 2000

Clark's Fork River Drainage

East Fork Bull River Bank Stabilization and Channel Restoration
WATER NAME: East Fork Bull River - Clark Fork River
DATE PROVIDED BY: Laura Katzman and Pat Saffel, FWP
DETAILED REPORT CITATION: Katzman and Saffel (2001)
MFWPCODE: FFM1-1998

Channel restoration and bank stabilization are planned for a section of the East Fork of the Bull
River on Robert Stein's property. Fish population estimates were done in two sections during
2000, a portion of the channel within the proposed restoration area (Treatment) and upstream of
the proposed restoration area (Control). The proposed Treatment area supported westslope
cutthroat, brown, brook, and bull trout, as well as mountain whitefish and sculpin. Only two
small bull trout were captured, so an estimate was not computed for them. The Control Section
supported westslope cutthroat trout, bull trout, and sculpin. The Control Section supported
significantly higher populations of westslope cutthroat and bull trout than did the Treatment
Section (Figure 12). In addition to population estimates, weirs and traps were operated just
downstream of the Stein property during the spring and fall of 2000 to monitor use of the portion
of the East Fork above these traps by spawning trout. Data from these traps have not yet been
summarized. Baseline data consisting offish population estimates and fish trap catches
have been collected prior to FFI activities.

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Species

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Figure 12. Number of westslope cutthroat (WCT), brown, brook, and bull trout estimated per
1,000 feet of channel length (standard deviations shown by vertical lines) in the
proposed FFI project area (Treatment) and a control area upstream during 2000.

Page A- 19
December 2000

Elk Creek Channel Restoration

WATER NAME: Elk Creek - Clark Fork River
DATE PROVIDED BY: Pat Saffel, FWP
DETAILED REPORT CITATION: Saffel (2001)

MFWPCODE: FFI-49-1996

The lower portion of Elk Creek, a tributary to the Clark Fork River near Heron, Montana, was
rehabilitated in late 1997. Rehabilitation consisted of bank stabilization and channel
reconstruction. The stream supports populations of brook and westslope cutthroat trout. The
objective was to increase numbers of trout, especially westslope cutthroat trout. Monitoring of
fish populations found that trout populations went up dramatically in the two upper restoration
sections (BS2 and New 2; Figure 13) following restoration activities in 1997. Population
increases in the lower two restoration sections were more modest and it appeared that trout may
have moved between the lower bank stabilization section (BS1) and lower channel restoration
section (New 1) in 2000 (Figure 13). It was clear that fish populations in all sections appeared to
increase more, and more consistently, than populations in the Control Section. Preliminary
data suggests that this FFI project has increased fish populations in the treatment areas.

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Control

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Figure 13. Number of trout (westslope cutthroat and brook trout combined) estimated for five
sections of Elk Creek in 1997 (pre-project) and from 1998 to 2000 (post-project).
Estimates were made in two bank stabilization treatment sections (BS 1 and BS2), two
sections where the channel was reconstructed (New 1 and New 2), and one control
section in a Wilderness Area (Control).

Page A-20
December 2000

Prospect Creek Channel Restoration

WATER NAME: Prospect Creek - Clark's Fork River
DATE PROVIDED BY: Laura Katzman and Pat Saffel, FWP
DETAILED REPORT CITATION: Katzman and Saffel (2001)
MFWPCODE: FFI-53-1999; FFI-24-2000

Redd count surveys were conducted in the fall of 1999 and 2000 from the upstream end of the
canyon below Clear Creek to Coyote Gulch. In 1 999 40 redds were observed and in 2000 30
redds were observed in this portion of the creek. Each year about half of the redds were thought
to have been constructed by brown trout and half by brook trout based on size of redds. In 1999
about 18% of the redds were located in the portion of restored channel and this restored portion
of channel made up about 20% of the total survey section. In 2000 about 17% of the redds were
located in the restored channel area, but during this year the restored channel made up about 25%
of the surveyed area. Redd count and distribution data has not indicated a response by spawning
fish to selectively use the restored portions of Prospect Creek immediately after restoration.
However, it may take some time before adequate cover for spawning fish develops; streambed
materials are sorted by high spring flows to provide good spawning gravels; and for spawning
fish to shift their spawning to these areas. A rotary screw trap operated just upstream of the
confluence of Dry Creek from March 9 to October 20, 2000 and a weir was operated just
downstream of the confluence of Dry Creek from August 8 to November 26, 2000. Data from
these traps have not yet been summarized, but will provide information on spawning fish moving
into and out of Prospect Creek and juvenile trout emigrations from the stream. Trapping and
redd count information from subsequent years will allow for evaluation of the effects of channel
restoration on fish reproduction and recruitment to the system. Populations offish were
monitored in four sections of Prospect Creek in 1999 and 2000. The lowermost section (mile
1 1 .0) had no flow during either year. Estimates in the other three sections illustrated that bull
trout populations declined slightly at mile 15, were the same at mile 17 and increased at mile
18.5, while populations of westslope cutthroat trout declined at mile 15, increased slightly at
mile 17, and declined slightly at mile 18.5 (Figure 14). Information collected currently
suggests that spawning fish have not yet responded to channel restoration in Prospect
Creek; however, it is probably too soon after restoration to reach any conclusions.

Rock Creek (Garrison) Instream Flow and Habitat Improvement Project Channel

WATER NAME: Rock Creek - Clark's Fork River
DATE PROVIDED BY: Eric Reiland, FWP
DETAILED REPORT CITATION: Rieland (in prep.)
MFWPCODE: FFI-20-1999

The Rock Creek Instream Flow and Habitat Improvement Project converted the Garrison
Ranch's flood irrigated pastures to sprinkler irrigation and all salvaged water was donated for
instream flow (5-27 cfs). The lower 1 .75 miles of Rock Creek had been annually dewatered for
the past 35 years. The project also restored four meanders using bank stabilization and channel
reconstruction techniques to create 46 new pools and 16 areas with overhead cover. The purpose
of the channel restoration and instream flow water lease was to provide spawning opportunities
for trout from the Clark Fork River and improve habitat for resident salmonids.

Page A-21
December 2000

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Species (Mile)

Figure 14. Numbers of bull (BT) and westslope cutthroat trout (WCT) estimated per 1,000 feet
of stream length by stream mile in 1999 and 2000. The FFI channel restoration
projects were located at mile 17.

Fish evaluations for this project include redd counts and electrofishing population estimates.
During the fall of 2000, brown trout redds were counted for a 2.5 mile reach of Rock Creek
affected by the project. Redd surveys were made three times during the fall at intervals of at
least one week. These surveys indentified 4 definite redds, 9 probable redds and 4 test digs.
Electrofishing estimates will be conducted during the summer 2001 field season. Baseline redd
counts have been conducted and fish population estimates are planned to evaluate this
project.

Jefferson River Drainage

Hell's Canyon Creek Irrigation Modification

WATER NAME: Hell's Canyon Creek - Jefferson River

DATE PROVIDED BY: Ron Spoon, FWP

DETAILED REPORT CITATION: No report available (FWP files, Townsend, MT)

MFWP CODE: RRA-38-93

Page A-22
December 2000

Improvements to an irrigation withdrawal system in Hell's Canyon Creek during 1997 have
eliminated the loss of juvenile trout down an irrigation ditch on lower Hell's Canyon Creek. A
screen by-pass of the irrigation diversion allows juvenile rainbow and brown trout to move
downstream and into the Jefferson River. In addition, flows in Hell's Canyon Creek below the
irrigation diversion remained above 5 cfs in 1999 and above 1 cfs during 2000 (above the
required minimum of 0.25 cfs). Without flow augmentation negotiated as part of this project
Hell's Canyon Creek would have gone dry below the irrigation diversion in 2000. This project
has eliminated loss of juvenile trout to an irrigation ditch and provides flows that allow
these juvenile trout to emigrate from Hell's Canyon Creek into the Jefferson River.

South Willow Creek Bank Stabilization

WATER NAME: South Willow Creek - Jefferson River
DATE PROVIDED BY: Brad Shepard, F WP
DETAILED REPORT CITATION: Shepard (2000a)
MFWP CODE: FFI-29-2000

FFI funds are proposed for stabilizing stream banks and to build a fence that excludes the
riparian area from livestock grazing along a portion of South Fork Willow Creek within the
Maichel's property near Harrison, Montana. Mark-recapture population estimates were
conducted using a mobile electrode system in a 2,460 feet-long Control Section above the
Maichel's property and in a 1,540 feet-long FFI Section within the Maichel's property on June
22, 2000. These estimates were conducted prior to any restoration work and represent pre-
treatment conditions.

The upper Control Section supported an estimated 652 (SD: 42; plus 2 mortalities that were 4.0
to 4.9 inches) brown trout and 91 (SD: 15) rainbow trout 3.0 inches and longer. Prior to bank
stabilization treatments the lower FFI Section supported an estimated 521 (SD: 59; plus 13
mortalitites that were 4.0 to 4.9 inches) brown trout and 278 (SD: 90; plus seven mortalities that
were 3.0 to 3.9 inches) rainbow trout 3.0 inches and longer. It should be noted that fish less than
5.0 inches in length (fish age 1 and younger) dominated the populations, particularly for the
lower treatment section (Figure 15). For fish 6 inches and longer the estimates were 258 and 310
for brown trout in the lower FFI and upper Control sections, respectively, and 39 for rainbow
trout in both sections. When these estimates were standardized to number offish 6.0 inches and
longer per 1 ,000 feet of stream length the lower FFI Section supported more fish per stream
length for both species than the upper Control Section (Figure 16).

Length frequency histograms illustrated that both sections supported rainbow trout up to about
12 inches and brown trout up to about 17 inches (Figure 15). Length frequencies of captured fish
were similar between sections. Baseline fish population data have been collected prior to the
construction of the FFI project in South Willow Creek. These data found that fish
populations were slightly higher in the proposed treatment portion of South Willow Creek
than in an upstream control portion that is not scheduled to be treated.

Page A-23
December 2000

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0 2 4 6 8 1 0 1 2 1 4 1 6 1 8 0 2 4 6 8 10 12 14

Length Class (0.5 inch) Length Class (0.5 inch)

15. Length frequency histograms for brown trout (left) and rainbow trout (right) captured
in an upper Control Section (top) and lower FFI Section (bottom) of South Willow
Creek in 2000.

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6.0 + inches by species

2000

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Figure 16. Estimated number and standard deviations (vertical lines) of brown trout (left) and
rainbow trout (right) 6.0 inches and longer in both a section where FFI funds will be
spent on bank stabilization (FFI Section) and in an upper Control Section of South
Willow Creek during 2000.

Page A-24
December 2000

Judith River Drainage

Big Springs Creek Brewery Flats Channel Restoration

WATER NAME: Big Spring Creek - Judith River
DATE PROVIDED BY: Anne Tews, FWP
DETAILED REPORT CITATION: Liknes et al. (In prep.)
MFWPCODE: FFI-24-1997

Big Spring Creek in the Brewery Flats area consisted primarily of a straight, rock-lined channel
with high velocities due to channelization. FFI funds were used to restore a more natural
meandering channel-type by lengthening this section of channel. Mark recapture data for trout
populations were collected in August or September from 1995 to 2000 from three sections of Big
Spring Creek. Sites included the Burleigh (5860 feet) and Brewery Flats (3704 feet) sections
above Lewistown, and the 4394-foot Carroll Trail (Tresch) section below town. In 2000, a 3740-
foot section was electrofished at Carroll Trail. Historical population data was also analyzed from
1967, 1968 and 1982. The Tresch and Burleigh sections have a somewhat natural meander
pattern and are considered control sections for this project. After sampling in September 2000,
2500 feet of the Brewery Flats Section was re-routed into a restored channel. Habitat
information has been collected, but has not been summarized, from the old straightened channel.

Estimates of small (6 to 10 inches) rainbow trout were typically lowest in the Burleigh section
(Figure 17). Estimates of larger (10 inches and longer) trout per mile from the Brewery Flats and
Burleigh sections were similar with overlapping confidence intervals. Below town (Tresch),
estimates were consistently higher for both brown and rainbow trout than in either section above
town. For example, from 1995 to 2000, estimates for larger rainbow trout (10 inches and longer)
fluctuated from 874 to 2453 per mile below town at the Carroll Trail section, but were only 207
to 622 per mile in the Burleigh section and 218 to 756 per mile at the Brewery Flats section. In
2000 record high numbers of trout, approximately 3231 trout 10 inches and longer (3222
pounds) per mile, were found in the Carroll Trail section. This compares with point estimates of
726 (703 pounds) and 1039 (756 pounds) per mile for the Burleigh and Brewery Flats section,
respectively. The FFI project for Brewery Flats increased channel length and this increased
channel length will probably result in higher overall populations of fish in this segment of
stream, even if fish densities (number offish per acre or mile) stay the same as in the old
channelized portion of channel. It is anticipated that fish densities will also increase in this
channel segment due to improved habitat conditions. Presently the average size for age 2 and
older rainbow trout appears to be smaller (almost an inch shorter for average length) in the
restoration section than in the other two sections. Baseline data have been collected to
evaluate the FFI project for the Brewery Flats channel restoration.

Page A-25
December 2000

1200

1000

800

600

400

200

1967

1968

1982

1995

1996

1997

1998

1999

2000

Figure 17. Estimated number and 95% confidence intervals (vertical lines) of rainbow trout 10
inches and longer per mile in three sections of Big Springs Creek from 1967 to 2000.

Cottonwood Creek Channel Restoration

WATER NAME: Cottonwood Creek - Judith River
DATE PROVIDED BY: Brad Shepard, FWP
DETAILED REPORT CITATION: Shepard (2000b)
MFWP CODE: FFI-9-2000

On July 10 and 11, 2000, prior to construction of a channel restoration project on Floyd
Maxwell's property funded by Future the Fisheries Improvement program, a depletion fish
population estimate was made in two sample sections in Cottonwood Creek (a tributary to the
Judith River near Lewistown, Montana) within Floyd Maxwell's property. Sampling was
conducted in a 1,150-feet-long section of Cottonwood Creek within the proposed restoration area
(FFI Section) and another 1,150-feet-long control (Control Section) above the restoration
section, starting at the upper fenceline and continuing downstream past the shooting range on the
Maxwell Ranch. Depletion fish population estimates were made for fish 3.0 to 5.99 inches, 6.0
to 1 1.99 inches, and 12.0 inches and longer.

The FFI Section supported primarily brook trout, while white suckers, sculpins and longnose
dace were also observed, but not estimated. A four-pass depletion estimate for this 1,150-foot
long section resulted in estimates of 36 (SD: 1.1) brook trout 3.0 to 5.99 inches, 47 (SD: 2.4)
brook trout 6.0 to 1 1.99 inches, and 2 (SD: 0.6) brook trout 12.0 inches and longer prior to any
channel restoration. The Control Section also supported primarily brook trout; however, while

Page A-26
December 2000

sculpins were commonly observed, white suckers and longnose dace were less abundant than in
the FFI Section. A three-pass estimate for the 1,150-foot long upstream Control Section resulted
in estimates of 60 (SD: 13.9) brook trout 3.0 to 5.99 inches, 93 (SD: 4.2) brook trout 6.0 to 1 1 .99
inches, and 2 (SD: 0.4) brook trout 12.0 inches and longer. Numerous young-of-the-year brook
trout less than 3.0 inches were observed, but not estimated in both sections. When estimates of
fish 3.0 inches and longer were standardized to the number per 1,000 feet of stream length, it was
obvious that the Control Section supported significantly higher populations of brook trout than
the proposed FFI restoration section (Figure 18). Most captured brook trout from both sections
were 4 to 10 inches; however, more longer (>6.0 inches) brook trout were captured in the
Control Section than in the FFI Section, but both sections supported brook trout over 12 inches
(Figure 19). Baseline fish population data have been collected prior to the construction of
the FFI project in Cottonwood Creek. These data found that fish populations were higher
in the control portion than in the proposed treatment portion of Cottonwood Creek.

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Brook Trout 3.0 inches and long

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120 -

100 -
80 -

60 -

40 -

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Control

Section

Figure 18. Estimated numbers (standard deviations shown as vertical capped lines) of brook

trout (standardized to number per 1,000 feet of stream channel) 6.0 inches and longer
in a FFI habitat restoration section and Control section of Cottonwood Creek in 2000.

Page A-27
December 2000

tsssssa Control
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3 4 5 6 7 8 9 1011 121314

Length Class (0.5 inch)

Figure 19. Length frequencies for brook trout captured in the FFI Section (cross hatch bars) and
a Control Section (grid bars) of Cottonwood Creek in 2000.

Missouri River Drainage

Canyon Ferry Yellow Perch Habitat Enhancement

WATER NAME: Canyon Ferry Reservoir - Missouri River
DATE PROVIDED BY: Dave Yerk, FWP
DETAILED REPORT CITATION: Yerk (In prep.)
MFWP CODE: FFI-35-1998

Monitoring was initiated in 2000 to evaluate the use of Christmas trees placed in Canyon Ferry
Reservoir to enhance yellow perch spawning and rearing habitat in the reservoir. An underwater
camera was used to visually inspect trees for deposition of perch skeins and to monitor use of
trees by juvenile fishes later in the summer. Additionally, two clusters of 'sentry' trees were
placed at the Silos where turbid water conditions precluded the effective use of the camera.
Marked with buoys, these trees could be pulled to the surface and inspected for egg skeins. The
Silos site 'sentry' trees were checked weekly following their deployment in early April. No eggs
were observed on these trees until May 9 (1 1.0 C), when 8 skeins were observed on one of the
structures. Eggs were never observed on trees deployed at the White Earth and Hellgate sites.
Trees placed at these sites sunk to the bottom within about a month of deployment. Because the
White Earth and Hellgate sites were located in bays where little wave activity washed over the
trees, silt and periphyton may have accumulated rapidly on branches and needles causing them to
sink. The trees at the Silos site remained relatively clean and stood upright through August.
Juvenile fish were not documented using the structures at any of the sites for rearing habitat.
Because the reservoir is at full-pool in July and August, the trees are likely too deep to provide

Page A-28
December 2000

rearing habitat. Beach seine sampling completed in late August did not show any notable
changes in age-0 perch production from previous years. However, we are still evaluating the
validity of this methodology for providing a baseline of age-0 yellow perch production. Based on
this year's observations, efforts in spring 2001 will be directed at increasing the number of
structures placed in the south end of the reservoir (Silos site). Trees placed in the reservoir at
other sites will be deployed in the main reservoir and not in bays. Efforts to monitor use of the
structures by spawning perch will continue with the placement of 'sentry' trees and the use of the
underwater camera. Perch may use placed underwater trees for spawning, but extensive use
of these trees by spawning perch was not yet documented. No documentation is yet
available that shows these trees are being used by juvenile fish.

Highwood Creek Channel Rehabilitation
WATER NAME: Highwood Creek- Missouri River
DATE PROVIDED BY: Brad Shepard, FWP
DETAILED REPORT CITATION: Shepard (2000c)
MFWP CODE: FFI-12-1998

Baseline fish population sampling conducted in 1997 and 1998 was reported in Shepard (1998).
Between July 1998 and June 30, 1999 the FFI bank stabilization and channel restoration project
on John McGowan's was completed. On June 30, 1999 a mark-recapture estimate made 656-
foot Control section located above the FFI treated section estimated 1 14 brown trout (SD: 13.7)
and 52 brook trout 5.0 inches and longer (SD: 4.6) occupied this section. No reliable estimate
could be made for rainbow trout in the Control section. The 863-foot long FFI restoration
section supported an estimated 217 brown trout (SD: 9.6), 67 brook trout (SD: 4.7), and 39
rainbow trout 5.0 inches and longer (SD: 5.5). During the summer of 1999 Highwood Creek was
badly dewatered and the "Control" section was reported to have gone totally dry, while the "FFI"
section retained some flow due to the presence of several springs near the upper end of this
section (personal communication, George Liknes, Montana FWP, Great Falls and John
McGowan, Highwood). On July 12, 2000 the FFI section supported an estimated 228 (SD: 2.9)
brown trout, 24 (SD: 5.8) rainbow trout, and 22 (SD: 0.5) brook trout 6.0 inches and longer,
while the Control section supported an estimated 16 (SD: 0.9) brown trout, one (all fish captured
on first pass) rainbow trout, and 16 (SD: 0.6) brook trout 6.0 inches and longer. Prior to 2000
sampling we removed a beaver dam within the Treatment section that had created a beaver pond
that inundated about 100 feet of the channel. The impact of the dewatering of the Control
section in 1999 on the fish populations was obvious from the low numbers offish found in this
section in 2000.

When estimates were standardized to number offish 6.0 inches and longer per 1,000 feet of
stream channel it was apparent that numbers of brown trout increased from 1997 to 2000;
rainbow increased from 1997 to 1999, but declined slightly in 2000; and brook trout have
steadily declined since 1998 within the FFI treated portion of channel (Figure 20). Brown trout
numbers have remained higher in the FFI treated portion than the Control portion; however,
dewatering of the Control portion in 1999 influenced these results. It appears that the FFI habitat
restoration enhanced brown trout; however, brook trout numbers have declined. Brook trout
declines were probably related to increased competition with a larger population of brown trout
that were increasing because of habitat restoration. The dewatering that occurred in 1999 within

Page A-29
December 2000

the Control section makes it difficult to attribute increases within the FFI treated section solely to
habitat restoration. The differential impact of dewatering on these two sections will confuse
efforts to evaluate the habitat restoration project.

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Fish Estimates

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97 98 99 00
Brown Trout

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Rainbow Trout

Species and Year

97 98 99 00
Brook Trout

Figure 20. Numbers (standard deviations shown as vertical capped lines) of brown trout,
rainbow trout, and brook trout (standardized to number per 1 ,000 feet of stream
channel) 6.0 inches and longer estimated for a FFI habitat restoration section and
Control section of Highwood Creek from 1997 to 2000.

In an effort to understand how these two sections might be utilized for spawning and early
rearing the relative catches (number caught on first electrofishing pass) offish less than 6.0
inches per 1,000 feet of stream were plotted for 1999 and 2000, the years fish less than 6.0
inches were captured (Figure 21). It appears that rainbow trout are not using this portion of the
stream for spawning, as almost no young rainbow trout were captured. It was interesting to see
the dramatic increase in relative catches of both brown and brook trout within the FFI treated
section from 1999 to 2000, in spite of the extremely low water experienced in 1999. This type of
increase was also seen in the Control section for brook trout, but not for brown trout. It may be
that the decline in brook trout 6.0 inches and longer might be a temporary situation and with the
good reproduction that appears to have occurred in 2000, more larger brook trout will inhabit the
FFI section in the future.

A few large brown trout were captured in both sections during each sampling event (Figure 22).
Numerous young-of-the-year brook and brown trout were captured during 1 999 and 2000 in each
section (Figure 22). Preliminary information suggests that the FFI channel restoration in
Highwood Creek has resulted in higher standing crops of trout; however, the de-watering
that occurred in 1999 has complicated interpretation of these results.

Page A-30
December 2000

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180 -
160 -
140 -
120-
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80

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99 00

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Figure 21. Relative catch (number offish captured on the first electro fishing pass per 1,000 feet
of channel length) for brown, rainbow, and brook trout less than 6.0 inches long in a
FFI habitat restoration section and Control section of Highwood Creek in 1999 and
2000.

Rainbow Trout
1999

0123456789 1011121314151617181920 0 , 2 3 4 5 6 7 8 9 10 11 12 13 14 15 0 1 2 3 4 5 6 7 8 9 10 1 1 12 13 14 15
Length Class (0.5 inch) Length Class (0-5 inch) Length Class (0.5 inch)

Figure 22. Length frequencies for brown trout (left), brook trout (middle), and rainbow trout

(right) captured in the FFI project area (cross hatch bars) and a control area (grid bars)
of Highwood Creek in 1999 (top) and 2000 (bottom).

Page A-3 1
December 2000

Magpie Creek Fish Passage

WATER NAME: Magpie Creek - Canyon Ferry Reservoir - Missouri River
DATE PROVIDED BY: Ron Spoon, FWP

DETAILED REPORT CITATION: Shepard (1998); (FWP files, Townsend, MT)
MFWP CODE: FFI-54-96

Spawning site (redd) surveys conducted in Magpie Creek in 1997 and 1998 indicated that the
FFI project that modified a culvert by inserting a fish ladder allowed rainbow trout from Canyon
Ferry Reservoir to ascend Magpie Creek through the culvert to spawn (Shepard 1998). In 2000
beaver dams located in the lower 2 miles of Magpie Creek and extremely low spring flows and
low reservoir levels in Canyon Ferry Reservoir led to no rainbow trout being observed in the
vicinity of the culvert and no redds were observed above the culvert. Preliminary data found
that rainbow trout spawners from Canyon Ferry Reservoir were ascending Magpie Creek
to spawn above the culvert retrofitted with a fish ladder; however, low flows and beaver
activity in 2000 resulted in no spawning use of Magpie Creek above the culvert.

Missouri River Bank Stabilization - Range and Below Craig

WATER NAME: Missouri River
DATE PROVIDED BY: Brad Shepard, FWP
DETAILED REPORT CITATION: Shepard (2000d)
MFWP CODE: RRA-73-1995, FFI-21-1997 and FFI-16-1998

We attempted to quantify the relative effects of several bank stabilization projects completed on
the Missouri River by assessing the relative catch of fish along various river banks at night using
jet boat electrofishing and by conducting controlled angling sampling along various stream bank
sections during both 1998 and 1999. We assessed six different areas: barbs installed along
Range's property (Barb); an old riprapped bank above the Craig Bridge (Riprap); a natural
eroded bank near an irrigation pivot below the Craig Bridge (Natural Er); old barbs installed on
Sterling's property (Old Barb); debris and channel stabilization along Judeman's property near
the 1-15 bridge (Debris); and a slightly eroded natural bank along Lehman's property below the
1-15 bridge (Natural; Figure 23).

During 1998 total catches of rainbow trout per 1,000 feet of bank were similar in all six areas,
however, catches of smaller rainbow were higher along the Riprap and Debris banks (Figure 23).
Catches of brown trout varied widely in 1998 with no apparent trend between treated and
untreated areas with the Riprap and lower Natural bank having the higher catch rates (Figure 23).
The lowest catch rates for brown trout in 1 998 were seen along the upper natural eroded bank

Page A-32
December 2000

1998 Rainbow

1998 Browns

Barb Riprap Natural Er Old Barb Debris Natural

Barb Riprap Natural Er Old Barb Debns Natural

30

25

•

* 20

o
o
o

fe 15

a

a
n

E 10

3

5

1999 Rainbow

< 6 inches
V////A 6 + inches

1999 Browns

Barb Riprap Natural Er Old Barb Debris Natural

Barb Riprap Natural Er Old Barb Debns Natural

Figure 23. Catch rates (number per 1,000 feet of river bank) for rainbow and brown trout less

than 6 inches and 6 inches and longer along six river bank sections along the Missouri
River near Craig, Montana.

Page A-33
December 2000

(Natural Er). In 1999 we captured rainbow trout at higher frequencies along the upper Barb and
Riprap banks than any of the lower banks (Figure 23). We did not see a similar higher catch of
smaller rainbow trout along the Riprap or Debris banks compared to other banks as we had
observed in 1998. Catch rates for brown trout in 1999 were very similar to catch rates in 1998,
except we caught more brown trout along the Debris bank in 1999 than in 1998. Catch rates in
1999 indicated that all stabilized banks had higher catches than the upper naturally eroded bank,
but were not generally higher than the lower slightly eroded natural bank.

We were unable to document any differences between banks in our angling survey; however, this
survey consisted of a single float down each bank in 1998 and two floats down each bank in
1 999. In 1998 we caught no fish along any of the treated banks and only had six strikes,
catching one rainbow and two mountain whitefish in the entire survey. During angling floats in
1 999 we captured several fish along each bank, but no trend was evident.

It appears that trout abundance along stabilized banks may have been somewhat higher than
along a highly eroded bank, but not higher than along a slightly eroded bank. Angling did not
appear to be a reasonable tool to sample differences in relative fish abundance along different
types of banks at the very low level of effort we expended. Angling might provide reasonable
data at a much higher level of effort. We wanted to assess angling success along different types
of banks because one rationale used by the project proponents for creating structure along
riverbanks was for improving angling success. Annual variability in night shocking catch rates
might cloud any conclusions that could be made from catch per effort sampling between bank
types. We suggest either conducting a much more intensive study on the effects of bank
stabilization techniques on fish; assuming that annual variability is minor and use catch per effort
to compare banks; or discontinue attempts to evaluate bank stabilization techniques on fish
abundance in large rivers. If the second option above is selected, we recommend conducting
catch per effort sampling during the same time period each year to minimize potential seasonal
variation. We further recommend that several years pre- and post-project completion will
probably be needed to account for some level of annual variation. We could not conclude that
these bank stabilization projects have led to higher populations or abundance offish. The
data suggest that brown trout were more abundant along the riprap bank than other bank
types; however, the natural bank had the next higher abundance of brown trout.

Missouri River Big Springs Spawning Channel

WATER NAME: Missouri River above Townsend
DATE PROVIDED BY: Ron Spoon, FWP

DETAILED REPORT CITATION: No report available (FWP files, Townsend, MT)
MFWP CODE: RRA-21-92

A spawning channel was constructed at Big Springs along the Missouri River in 1 994 to increase
spawning habitat for brown and rainbow trout inhabiting the Missouri River and Canyon Ferry
Reservoir. Redd (spawning site) counts were made during the fall (to count brown trout redds)
and spring (to count rainbow trout redds) from 1994 to 1998. No count was made during the
spring of 1996 and counts of rainbow trout redds made during the springs of 1997 and 1998 were
not complete counts due to turbid water making redd observation extremely difficult. In 1998,
no counts of brown trout redds were made after November 19, so the count for brown trout in

Page A-34
December 2000

1998 was an incomplete count. Both brown and rainbow trout were using the new spawning
channel immediately following its construction (Table 1). The number of brown trout redds
declined somewhat after 1995; however, this area has been used as a source for taking brown
trout eggs as part of the Toston Mitigation Project and that may explain the reduced number of
redds. More brown trout redds were observed in 1999 than in any other year. No significant
changes in the constructed spawning channel have been observed since its construction in 1994.
The data indicate both brown and rainbow used this spawning channel immediately after
its construction. The number of observed redds has declined in recent years and the reason
for this decline is undetermined at this time.

Table 1. Number of brown and rainbow trout redds observed in the Big Springs spawning
channel of the Missouri River from 1994 to 1999.

Number of Redds

Year Season (dates of surveys)

Browns

Rainbows

44

.

44

-

-

10337

43

.

-

15b/

51

.

-

16c/

18

-

.

57c/

13c/

.

1993 Fall (10/14 -1/19)

1994 Fall (10/25 -12/23)

1995 Spring (2/16 -5/8)
Fall (11/6- 12/20)

1996 Spring (4/10)
Fall (10/26 -12/18)

1997 Spring (4/2)
Fall (11/3 -12/16)

1998 Spring (3/17 -4/15)
Fall (10/28 -11/19)

1999 Spring (3/23 -5/18) 30
Fall (10/26 -12/6) 57

^ Represents the minimum number due to sampling problems.
b Only a single survey was completed.

c/ Incomplete counts due to turbidity limiting visibility or because surveys were not done
through the spawning season.

White's Gulch Rehabilitation and Barrier

WATER NAME: White's Creek - Canyon Ferry Reservoir - Missouri River
DATE PROVIDED BY: Brad Shepard and Ron Spoon, FWP
DETAILED REPORT CITATION: Shepard and Spoon (in prep.)
MFWP CODE: RRA-74-1995 and FFI-16-1996

White's Creek in White's Gulch supports a genetically pure population of westslope cutthroat
trout. The RRA and FF1 projects in White's Gulch were part of a large cooperative effort to
reclaim White's Gulch from past mining impacts and conserve the existing population of
westslope cutthroat trout. In 1993 we began removing brook trout from a portion of White's
Creek above the area most heavily impacted by past placer and dredge mining (Above Project
area). In 1994 and 1995 the dredge and placer-mined portion of the White's Gulch valley and

Page A-35
December 2000

the stream channel were rehabilitated (Project area). A permanent fish barrier was placed about
1,000 feet below this rehabilitated segment of stream in 1995 (portion of the stream from this
barrier up to the Project area termed Below Project area). From 1995 through 1998 fish surveys
and brook trout removals were conducted from this permanent fish barrier up through the
rehabilitated portion of the channel. Fish sampling was conducted in three major areas of the
stream from 1993 through 2000. Catch of trout per 1,000 feet in each of these areas showed that
brook trout abundance declined significantly until only four brook trout were captured above the
constructed barrier during 2000 (Figure 24). Removal of brook trout and the restoration of the
stream channel have resulted in much higher catches of westslope cutthroat trout after 1995
(Figure 24). Observations and nearly total removal of brook trout from above this
constructed barrier indicate that brook trout cannot pass over the barrier. Habitat
restoration in the portion of White's Creek impacted from past mining activities has
dramatically increased the relative catch of westslope cutthroat trout in this portion of the
creek.

350

94 95 96 97 98 99 00 93 94 95 96 97 98 99 00 93 94 95 96 97 98 99 00

Below Project In Project Above Project

Figure 24. Relative catch (number of fish captured on the first electrofishing pass per 1 ,000 feet
of channel length) for westslope cutthroat and brook trout 3.0 inches and longer in
three areas of White's Gulch from 1993 to 2000.

Page A-36
December 2000

Musselshell River

South Fork Musselshell Irrigation Diversion Fish Passage
WATER NAME: South Fork Musselshell River- Musselshell River
DATE PROVIDED BY: Brad Shepard and Anne Tews, FWP
DETAILED REPORT CITATION: Shepard and Tews (2000)
MFWPCODE: FFI-28-2000

The Montana Department of Natural Resources and Conservation applied to provide fish passage
upstream over the Martinsdale Diversion dam on the South Fork of the Mussellshell River that
presently does not allow easy fish passage. Prior to modification of this irrigation diversion to
provide fish passage, a survey was conducted on October 1 7, 2000 to evaluate brown trout
spawning and movement above and below this diversion. A spawning site (redd) count was
done from the State Highway 294 bridge, near Martinsdale, upriver about 0.8 mile (includes
about 0.55 mile from the diversion to the highway and about 0.25 mile above the diversion).

On October 17, 2000 very little water was flowing down the South Fork Mussellshell below the
Martinsdale Diversion. No water was flowing over the diversion and the channel was
intermittent for about 0.2 miles below the diversion. Groundwater valley flow re-charged the
channel to create surface flow about 0.2 miles below the diversion, but flows were visually
estimated to be less than 2 cfs. Flows above the diversion were at least 10 cfs.

A total of three redds were observed below the diversion and two redds were seen above the
diversion. A total of six adult brown trout were observed below the diversion and three were
seen above the diversion. Two large redds were seen at the head of the diversion canal, just
below the diversion headgate. Spawning habitat above the diversion was under-utilized. A
large, well-maintained beaver dam blocked the entire channel about 0.25 miles above the
diversion. Below the diversion lots of good deep pool habitats were seen and several beaver
dams may partially block upstream movement offish, especially at low flows.

A total of 22 brown trout were captured in 840 feet of channel. These brown trout averaged 14.1
inches long (range: 7.1-20.9) and 1.10 pounds (range: 0.2-2.0). Of these 17 were tagged with
number Floy tags to assess movement. Eight of the captured brown trout were identified as
females and six were identified as males that had either just recently spawned or were ready to
spawn. Water flows during summer and fall 2000 were some of the lowest on record. Fall flows
at Martinsdale Diversion must be adequate to fully water both the fish passage structure and the
river channel below the diversion to effectively pass fish. Baseline data have been collected to
evaluate whether a proposed fish passage facility at the Martinsdale Diversion allows
brown trout to move above the diversion and results in additional spawning above the
diversion.

Page A-37
December 2000

Sun River Drainage

Spring Coulee Bank Stabilization

WATER NAME: Spring Coulee Creek - Sun River
DATE PROVIDED BY: Brad Shepard, FWP
DETAILED REPORT CITATION: Shepard (2000e)
MFWP CODE: FFI-26-1998

A single electrofishing pass was made in Spring Coulee Creek on Mark Lee's property on July 1,
1998, prior to completion of the FFI bank stabilization project, and results from that effort were
reported in Shepard (1998). The FFI bank stabilization project was completed within the lower
section (New Treated) from the fall of 1 998 through the early summer of 1 999. On June 24,
1 999 we were able to conduct a mark-recapture estimate in the same three sections (Control, Old
Treated, and New Treated) that were sampled previously. However, the lower section (New
Treatment) was about 1,900 feet longer than the 1,150 feet sampled in 1997. High turbid stream
flows during the mark run limited our capture efficiencies. We clipped different fins as marks
between the three sections to test for movement between sections. A mark-recapture estimate
was made across all three sections and then portioned within each section by the proportion of
total fish marked by species. Estimates were made for rainbow, brown, and brook trout.

In 1999 relative catches (number captured per 1,000 feet) were higher in all sections than
observed in 1998; however, the much higher catches in the Old and New Treatment sections
during 1 999 could be attributed to better sampling efficiencies related to cooler water
temperatures (Figure 25). Brook trout were only captured in the lower section in 1998, but were
captured in all sections during 1999. Mark-recapture population estimates made using the
modified Peterson estimator in 1999 estimated that the entire 5,550-foot long sample section
supported 60 (SD: 8.0) brown trout 8.0 to 28.9 inches long, 84 (SD: 1 1.5) rainbow trout 1 1.0 to
23.9 inches long, and 35 (SD: 10.7) brook trout 6.0 to 13.9 inches long. When these estimates
were apportioned between the three sample sections based on proportion of fish marked in each
section, it was apparent that the New Treatment Section had the highest estimated number of
trout (Figure 26). Since population estimates were done immediately following the FFI bank
stabilization in the New Treatment section, these estimates should be regarded as pre-treatment
estimates for this section. Six of the 1 5 recaptured brown trout and two of 1 5 recaptured rainbow
trout were recaptured in a different sub-section than where they were tagged, indicating that
movement, particularly by brown trout, occurred between sub-sections in between the mark and
recapture events. Half the fish moved upstream (3 browns and 1 rainbow) and half moved
downstream (3 browns and 1 rainbow). Many of the rainbow and brown trout within this portion
of Spring Coulee Creek were over 1 8 inches with some over 24 inches (Figure 27). Rainbow
trout averaged 14 to 20 inches, brook trout averaged 8 to 10 inches, and brown trout averaged 17
to 25 inches in length.

Page A-38
December 2000

o
o

25

~ 20

f////i Browns
Rainbows
Brook

98 99
Control

98 99
Old Treatment
Year
Section

98 99
New Treatment

Figure 25. Relative catches (number captured in first pass per 1,000 feet) of rainbow, brown and
brook trout in three sections of Spring Coulee Creek in 1998 and 1999. Note that in
1 998 warm water temperatures limited catch efficiencies in the Old and New
Treatment sections.

During July 2000 we observed that livestock exclusion fences had been constructed along the
entire length of stream on Mr. Lee's property including a few water gaps and a ford.

In conclusion, this portion of Spring Coulee Creek supports relative low populations of very
large trout. It appears that recruitment of rainbow trout from within this area of Spring Coulee
Creek is very limited based on length frequency information (Figure 26). It is possible that large
trout move into this portion of the creek from downstream areas during the summer, but more
detailed movement data would need to be collected to confirm this speculation. These data will
serve as reasonable baseline data for evaluating the FFI funded bank stabilization project. The
1998 data provide baseline data on fish in Spring Coulee Creek and indicate relative
abundance's were similar between untreated and treated sections and that this stream
supports some large rainbow and brown trout.

Page A-39
December 2000

^ 50

O
O

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111

40 -

o

Q- 30

0)

| 20

w 10
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0

Ezzzi Browns
i i Rainbow
■hh Brook Trout

Control

Old Treatment

New Treatment

Section

Figure 26. Estimated number of brown trout (8 inches and longer), rainbow trout (1 1 inches and
longer) and brook trout (6 inches and longer) per 1 ,000 feet of stream length in three
sections of Spring Coulee Creek within Marc Lee's property during June 1999.

Page A-40
December 2000

JZ 5
(A

il4
o

i- 3
o

|2

Z 1

Spring Coulee Creek - 1998

■ Brook

■ Brown
□ Rainbow

M ; I i i i ; i

0 2 4 6 8 10 12 14 16 18 20 22 24 26 28

Length Class (0.5 inch)

Spring Coulee Creek - 1999

(/>

O 5
O 4

E 3

■ Brook

■ Brown
□ Rainbow

■T T T T ( 1 r —

0 2 4 6 8 10 12 14 16 18 20 22 24 26 28

Length Class (0.5 inch)

Figure 27. Length frequencies for brook (solid bars), brown (cross-hatched bars), and rainbow
(stippled bars) trout in three sections of Spring Coulee Creek sampled in July 1998
(top) and June 1999 (bottom).

Page A-4 1
December 2000

Sun River Inventory and Design - Simms to Fort Shaw; Bank Stabilization

WATER NAME: Sun River- Missouri River

DATE PROVIDED BY: Brad Shepard, Bill Hill, George Liknes and Steve Leathe, FWP

DETAILED REPORT CITATION: Hill et al. (in prep.)

MFWP CODE: FFI-22-1997, FFI-46-1997, FFI-47-1997, FFI-24-1999, FFI-31-2000

A pilot study was done in 1997 to determine the effort needed to estimate fish populations in
several sections of the Sun River (Shepard 1998). In 2000 mark-recapture population estimates
were done for the Sun River below the towns of Augusta and Sun River. These sampling efforts
obtained relatively poor quality population estimates; however, these data consistently suggest
that the Sun River supports relatively low population densities of rainbow and brown trout and
that population levels appear to decrease in a down river direction. In addition, the Sun River
supports some relatively large brown trout. It is believed that the principal factor limiting trout
populations are low summer river flows. Preliminary data indicate that fish densities are
relatively low in the Sun River, trout abundance decreases in a down river direction, the
river supports some large brown trout, and low summer flows are likely limiting trout
populations at the present time.

Yellowstone River Drainage

Big Creek Irrigation Efficiency

WATER NAME: Big Creek - Yellowstone River

DATE PROVIDED BY: Leanne Roulson, Garcia and Associates

DETAILED REPORT CITATION: Roulson (2000)

MFWP CODE: FFI-27-1998

A water lease linked to improving irrigation efficiency in the lower Big Creek drainage was
initiated in 1 999. This lease provides water to lower Big Creek to improve the success of
spawning trout, primarily Yellowstone cutthroat trout (YCT), from the Yellowstone River in
lower Big Creek. Fry trapping to monitor this lease began in Big Creek in 1999. About 3,500
YCT fry were captured in 1999 during 35 days of trapping while over 1 1,000 fry were trapped in
2000 during 44 days of trapping (Figure 28). Compared to other tributaries that contribute YCT
fry to the Yellowstone River, Big Creek produced a relatively high total catch and catch per day
of YCT fry in 2000 (Figure 28). It is obvious that Big Creek has a high potential for
producing Yellowstone cutthroat trout to the Yellowstone River and the augmented flows
during 2000, a drought year, resulted in relatively high numbers of fry moving down into
the river.

Page A-42
December 2000

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Big Cedar

Stream

Mol Heron

Mol Heron

Figure 28. Total number (top) and catch per trap day (bottom) of Yellowstone cutthroat trout fry
captured in fry traps while emigrating from Mill, Big, Cedar, and Mol Heron creeks
from 1996 to 2000.

Page A-43
December 2000

Mol Heron Creek Flow Enhancement and Fish Screen
WATER NAME: Mol Heron Creek - Yellowstone River
DATE PROVIDED BY: Leanne Roulson, Garcia and Associates
DETAILED REPORT CITATION: Roulson (2000)
MFWP CODE: FFI-21-1996 and FFI-18-1997

A water lease and modification of an irrigation diversion in lower Mol Heron Creek drainage
was initiated in 1998. This lease provides water to lower Mol Heron Creek and the irrigation
diversion was modified to provide upstream passage to fish to improve the success of spawning
trout, primarily Yellowstone cutthroat trout (YCT), from the Yellowstone River in lower Mol
Heron Creek. Fry trapping to monitor this lease began in 1996. From about 1,100 to 4,100 YCT
fry have been annually captured from 1996 to 2000 during from 10 to 35 days of trapping
(Figure 28). Mol Heron Creek has the potential to provide some recruitment of
Yellowstone cutthroat trout to the Yellowstone River; however, the number of fry
emigrating during 2000 was less than 1999.

Stillwater River Channel Restoration

WATER NAME: Stillwater River - Yellowstone River
DATE PROVIDED BY: Brad Shepard and Mike Poore, FWP
DETAILED REPORT CITATION: None
MFWP CODE: FFI-30-2000

A 775-foot long side channel of the Stillwater River that had been cut off from the main channel
for years was reconnected and restored during the summer of 2000 to provide spawning habitat
to fish, primarily rainbow trout, from the Stillwater River. Prior to implementation of this
project, no water flowed in this channel. Immediately following construction, the channel was
surveyed on October 19, 2000 to check for evidence of brown trout spawing. There was no
evidence of spawning and no brown trout were observed; however, this result was expected since
the channel had been so recently restored. The newly restored channel contained plenty of
suitable spawning substrate with adequate water depth and velocity for spawning. There was
evidence of recent beaver activity in the channel. The landowners said that they had been
removing a dam that beaver were trying to construct near the mouth. No spawning could have
occurred in this channel prior to its restoration. This channel will need to be surveyed
periodically to document whether trout use this channel for spawning and, if so, the
number of redds constructed in the channel.

Page A-44
December 2000

Acknowledgements

Numerous biologists and field technicians from various agencies and Indian tribes contributed
significantly to this report. I would especially like to thank Montana FWP biologists Pat Byorth.
Chris Clancy, Bill Hill, Laura Katzman, George Liknes, Steve Leathe, Jim Magee, Lee Nelson,
Ron Pierce, Pat Saffel, Ron Spoon, Anne Tews, Joel Tohtz, and Dave Yerk; and technicians
Greg Hoffman and Paul Hamlin. David Barnes, Adam Sanhow, Tim Weis, and Paul Hamlin
assisted with fieldwork.

References

Clancy, C.G. In preparation. Statewide Fisheries Investigations. Bitterroot Forest Inventory.

Federal Aid Project F-46-R-4.Job Ij, Montana Fish, Wildlife and Parks, Helena, Montana.

Hunt, R. L. 1976. A long-term evaluation of trout habitat development and its relation to

improving management-related research. Transactions of the American Fisheries Society
105:361-364.

Katzman, L. M., and P. D. Saffel. 2001. Bull River Westslope Cutthroat Trout and Bull Trout
Life History Study, Report of Avista Corporation, Spokane, Washington.

Koopal, M. 1998. Stream habitat analysis of select tributaries to the Blackfoot River, 1998.
Report prepared for the Montana Fish, Wildlife and Parks, Missoula.

Liknes,G.A., A.E. Tews and W.J.Hill. In Preparation. Statewide Fisheries Investigations. North
central Montana Coldwater Streams. Projects F-78-R5; F-78-R6; and F-l 13-R1. Job
Progress Report. Montana Department of Fish, Wildlife and Parks. Fisheries Division.
Helena, Montana.

Peters, D. and R. Spoon. 1989. Preliminary fisheries inventory of the Big Blackfoot River.
Montana Department of Fish, Wildlife and Parks, Missoula.

Peters, D. 1990. Inventory of fishery resources in the Blackfoot River and major tributaries.
Montana Department of Fish, Wildlife and Parks, Missoula.

Pierce, R. and C. Podner. 2000. Blackfoot River fisheries inventory, monitoring and restoration
report 2000. Montana Fish, Wildlife and Parks, Missoula.

Pierce, R., C. Podner and J. McFee. In preparation. Blackfoot River fisheries inventory,

monitoring and restoration report 2001. Montana Fish, Wildlife and Parks, Missoula.

Pierce, R. and D. Schmetterling. 1999. Blackfoot River restoration project monitoring and
progress report: 1997-1998. Montana Fish, Wildlife and Parks. Missoula.

Page A -4 5
December 2000

Pierce, R., Peters, D. and T. Swanberg. 1997. Blackfoot River restoration progress report.
Montana Fish, Wildlife and Parks, Missoula.

Rosgen, D. 1996. Applied River Morphology. Wildland Hydrology, Pagosa Springs, Colorado

Roulson, L.H. 2000. Water leases and Yellowstone cutthroat trout fry outmigration from four
tributaries of the Upper Yellowstone River. Report by Garcia and Associates, Bozeman,
Montana prepared for Montana Fish, Wildlife and Parks, Helena, Montana.

Saffel, P. D., and Katzman, L. M. 2001. Prospect Creek Westslope Cutthroat Trout and Bull
Trout Life History Study, Report of Avista Corporation, Spokane, Washington.

Schmetterling, D. A. and R. W. Pierce. 1 999. Success of instream habitat structures after a 50-
year flood in Gold Creek, Montana. Restoration Ecology 7(4): 369-375.

Schmetterling, D. 1998. Timing of seasonal fluvial westslope cutthroat trout movement an
implications for management, Montana Fish, Wildlife and Parks, Missoula.

Schmetterling, D.A. 2000. Seasonal movement of fluvial westslope cutthroat trout in the
Blackfoot River drainage, Montana. Montana Fish, Wildlife and Parks, Missoula.

Shepard, B.B. 1998. Future Fisheries Improvement Program Monitoring Report - 2000.

Appendix A of Future Fisheries Improvement Program Report to 1999 Legislature and
Fish, Wildlife and Parks Commission, Habitat Protection Bureau, Fisheries Division,
Montana Fish, Wildlife and Parks, Helena, Montana.

Shepard, B.B. 2000a. South Willow Creek bank stabilization fisheries evaluation 2000.
Montana Fish, Wildlife and Parks, Helena, Montana.

Shepard, B.B. 2000b. Cottonwood Creek channel rehabilitation fisheries evaluation 2000.
Montana Fish, Wildlife and Parks, Helena, Montana.

Shepard, B.B. 2000c. Highwood Creek channel rehabilitation fisheries evaluation 1997 to 2000.
Montana Fish, Wildlife and Parks, Helena, Montana.

Shepard, B.B. 2000d. Missouri River bank stabilization: Range and Below Craig fisheries
evaluation 1998 and 1999. Montana Fish, Wildlife and Parks, Helena, Montana.

Shepard, B.B. 2000e. Spring Coulee bank stabilization fisheries evaluation 1998-1999.
Montana Fish, Wildlife and Parks, Helena, Montana.

Shepard, B.B. and R. Spoon. 2000. Westslope cutthroat trout restoration in Muskrat Creek,
Boulder River drainage, Montana: Progress report for period 1993 to 1999. Montana
Fish, Wildlife, and Parks, Helena, Montana.

Swanberg, T. R. 1996. The movement and habitat use of fluvial bull trout in the upper Clark
Fork drainage. MS thesis, University of Montana, Missoula.

Page A-46
December 2000

Swanberg, T. R. 1997. Movements of and habitat use by fluvial bull trout in the Blackfoot
River, Montana. Transactions of the American Fisheries Society 126:735-746.

Tohtz, J. 1996. Fisheries investigations in the Yellowstone and Shields River basins, Park

County, Montana. Progress Report for Federal Aid to Fisheries Projects F-78-R-1 and F-
78-R-2, Montana Department of Fish, Wildlife and Parks, Bozeman, Montana.

Page A -4 7
December 2000