Montana Fish, Wildlife and Parks Mark-Recapture Program

FISHERIES DIVISION Federal Aid Job Progress Report

Montana Statewide Fisheries Management

Federal Aid Project No: F-113-R1, R2, R3

Fiscal Year: July 1, 2003 – June 30, 2004 July 1, 2004 – June 30, 2005

Project Title: Statewide Fisheries Management Job Title: Bitterroot River Drainage Project Number: 3220 Project Reporting Period: January 1, 2003– December 30, 2004

ABSTRACT

Bitterroot River trout populations remained stable over the past few years with some exceptions. Rainbow trout in particular have declined in number in the upper river, but overall have increased slightly. Westslope cutthroat populations have increased since restrictive fishing regulations were imposed in 1990. The parasite associated with whirling disease, Myxobolus cerebralis was found in higher densities in the upper river particularly the East Fork Bitterroot. It may be the cause of declining rainbow trout numbers in the East Fork.

Fish population monitoring on the Bitterroot National Forest indicates that population trends vary throughout the drainage. No overall trend is apparent. The debris flows after the fires of 2000 had serious impacts to the fishery in some streams, but most seem to be recovering. Fishing regulation restrictions appear to be having a positive effect in Skalkaho and Daly Creeks

The stocking of Lake Como with kokanee has had mixed success. Early survival appeared to be high, however recent sampling has not identified much adult survival or spawning. Stocking of kokanee will be discontinued.

TABLE OF CONTENTS

BACKGROUND…………………………………………………………3

METHODS……………………………………………………………….4

RESULTS AND DISCUSSION…………………………………….……6

East Fork Bitterroot and Bitterroot River…………....…………...6 . Whirling Disease………………………………………….……..21

Radio Telemetry…………………………………………………23

Skalkaho Creek Ditches…………………………………………23

Bitterroot National Forest………………………………………..24

Lake Como………………………………………….……………42

LITERATURE CITED…………………………………….…….43

BACKGROUND

The Bitterroot River flows in a northerly direction from the confluence of the East and West Forks near Conner, Montana. The river flows 84 miles through irrigated crop and pastureland to it’s confluence with the Clark Fork River near Missoula, Montana. Five major diversions and numerous smaller canals remove substantial quantities of water from the river during the irrigation season (Spoon 1987). In addition, many of the tributaries, which originate on the BNF are diverted for irrigation during the summer months and contribute little streamflow to the river during that time. Therefore, many tributaries and the mainstem of the Bitterroot River are chronically dewatered during the irrigation season. Streamflow characteristics vary along the Bitterroot River, with the most critically dewatered reach between Hamilton and Stevensville (Spoon 1987). To help alleviate the mainstem dewatering, the MFWP annually supervises the release of 15,000 acre-feet of water from Painted Rocks Reservoir on the West Fork of the Bitterroot River and 3,000 acre-feet of water from Lake Como. Urbanization and associated development of the floodplain is increasing in the Bitterroot Valley (Javorsky 1994).

The Bitterroot River is an important sport fishery for anglers in western Montana. Pressure estimates from the statewide survey indicate that the Bitterroot River supported and estimated 92,150 angler days during 2003, (McFarland R.C. 2004). Due to the high fishing pressure, fishing regulations have become more restrictive in recent years to protect the adult fish. A creel census was conducted in 1992 and 1993 to assess these impacts. Overall, it indicated that fishing harvest was not having a serious impact on the population of trout but that monitoring should continue (Clancy 1993). Angling pressure has nearly doubled since that creel census. A Bitterroot River management plan is overdue since the original 5-year plan was written in 1991 (MFWP 1991).

Due to the importance of understanding connections between Bitterroot River salmonids and their spawning areas we implanted radio transmitters in westslope cutthroat trout Oncorhynchus clarki lewisi from the Bitterroot River in 2003. A private consultant and FWP personnel followed these fish to identify spawning locations.

Streams within the Bitterroot National Forest support widespread populations of native westslope cutthroat and bull trout. Due to the importance of streams within the Bitterroot National Forest (BNF), we have also monitored fish populations there. The Bitterroot National Forest encompasses 1.6 million acres, 71% of which is in Montana. Three mountain ranges, the Bitterroots to the west, the Sapphires to the east, and the Anaconda- Pintlars to the southeast comprise the Bitterroot National Forest. Water flowing within the BNF is excellent in quality and most is considered soft, a result of basin geology. Streams originating from the Bitterroot Mountains are unusually low in hardness and dissolved solids because of the resistant igneous and metamorphic rocks. The streams draining the Sapphire range tend to have higher dissolved solids because of slightly less resistant and more soluble background geology (Garn and Malmgren 1973). Within Montana, the BNF is the headwaters of the Bitterroot River.

During 2000, wildfires burned significant acreages in the Bitterroot drainage. It is estimated that 356,000 acres were burned. Studies of the impacts of wildfire on fisheries indicate that in healthy systems, most negative impacts are short-term (Gresswell 1999). Since wildfire impacts have been widely studied, we did not focus our work on assessing these impacts. However, a graduate study through Montana State University is researching the impacts of the fires on native and non-native trout. (Sestrich,in press).

Historically, Lake Como has been stocked with various species of fish. In the past decade catchable and brood rainbow trout have been stocked annually. Due to the fluctuating water levels in the reservoir, growth and survival has been poor. Beginning in 1997, kokanee, Oncorhynchus nerka, were stocked as fingerlings, in an attempt to add some variety for the anglers and study whether kokanee would grow faster than rainbow trout.

METHODS

Fish population estimates on the Bitterroot River were collected on several reaches over the past 23 years. Study reaches were selected based on historical data, streamflow patterns and fishing regulations. The reaches are 2.2-5.1 miles in length. Electrofishing was conducted from a 14-foot long aluminum drift boat fitted with a boom shocking system. The system was powered by 5000-watt generator and current was modified through a Coffelt Mark XXII electrofishing unit. Smooth direct current was used to capture fish. The Peterson mark-recapture method was used to calculate population estimates as modified through the Montana Fish, Wildlife and Parks mark-recapture program. Several mark and recapture runs were required to obtain sufficient sample size to estimate fish populations in some reaches. In recent years, most of the fish collections downstream of Hamilton have occurred at night to facilitate handling of more fish. The population estimates were collected during September and October each year. Brown trout may be migrating by October, therefore, their estimates may be inflated.

During 2003 and 2004 sentinel cages were used to assess the presence and degree of whirling disease. Personnel from the Bozeman office of MFWP installed the cages with the help of regional personnel. During this study period we concentrated on the East Fork and upper Bitterroot River.

A variety of ditches divert water from Skalkaho Creek. Some of the ditches divert water and fish directly from the creek while others mix Bitterroot River water and Skalkaho Creek water before diverting it from the creek. A graduate study was completed in 2003- 2004 to assess the impacts of ditches on fish. During 2004 fishscreens were installed in three of the ditches. The study also assessed the effectiveness of these screens.

We monitored fish populations in some streams on the Bitterroot National Forest. Background work that went into selection of the study sites is described in previous reports (Clancy 1993, 1996). Due to the severity and large geographic scale of wildfires on the Bitterroot National Forest in 2000 we selected our sites to assess some of the

4 future impacts. A graduate project was initiated to study the impacts of these fires on native and non-native fish populations (Sestrich, in press) Most of the sites chosen in the past few years are long term monitoring sites established previously. Fish were captured by electrofishing using smooth direct current. On larger streams a bank electrofishing unit is used powered by 4500 watt generator and current is controlled through a Coffelt VVP-15 unit. On small streams a backpack shocker, the Coffelt Mark 10, was used. We estimated trout populations on monitoring reaches using a mark-recapture technique. Monitoring sections are usually 1000 feet long. On the marking run, fish are released as close to their capture site as possible and approximately one week is allowed between mark and recapture. Population estimates are calculated using the Montana Department of Fish Wildlife and Parks Mark-Recapture program..

RESULTS AND DISCUSSION East Fork Bitterroot River and Bitterroot River

During 2003 and 2004 trout population estimates were collected from two sections of the lower East Fork of the Bitterroot River. During 2003 population estimates were collected on the Hamilton and Bell Crossing sections of the Bitterroot River. During 2004 population estimates were collected on the same East Fork Bitterroot River sections and the Hannon Memorial and Stevensville sections of the Bitterroot River (Figure 1).

Stevensville Bell Crossing

Hamilton

East Fork Bitterroot River 2.5 Hannon

East Fork Bitterroot River 12.0

3 10/22/2004

Figure1. Location of East Fork and Bitterroot River electrofishing sections discussed in this report.

Rainbow Trout

Overall, the rainbow trout population estimates indicate a positive trend in the number of rainbow trout, particularly in larger fish (Figures 3-12). One notable exception is the rainbow trout population in the lower East Fork Bitterroot (Figure 4.). In this reach, the rainbow trout population has been declining, possibly due to the presence of whirling disease. Whirling disease is discussed later in the report.

The rainbow trout estimates in the mainstem of the Bitterroot River indicate average populations of 8-12 inch fish and average to above average numbers of larger rainbow trout. Overall, rainbow trout populations are stable to increasing at this time, but may be vulnerable to whirling disease.

East Fork Bitterroot 12.0 Rainbow Trout

1200 2004 1000 2003 800 2002 600 95 2001 400 2000 2000 200 2002 97 0 2004 5 Year 6 7 8 9 95 Size Class

Figure 2. Population estimates of smaller rainbow trout in the East Fork Bitterroot 12.0 section during the years indicated.

7 East Fk Bitterroot 12.0 Rainbow Trout 2004 2003 100 2002 80 2001 60 2000 40 95 2000 20 97 2002 95 0 2004 10 11 Year 12 13 14+ Size Class (inches)

Figure 3. Population estimates of larger rainbow trout in the East Fork Bitterroot 12.0 section during the years indicated.

East Fork Bitterroot River 2.5 Rainbow Trout 2004 300 2003 200 2001 100 2000 0

98 98 5 6 7 8 9 10 11 12 13 14+ 2001 Year

Size Class (inches) 2004

Figure 4. Population estimates of rainbow trout in the East Fork

Bitterroot 2.5 section during the years indicated.

8 Bitterroot River-Hannon Memorial Rainbow Trout

2004

1500 96

1000 90 89 500

0 89 90

5 6 7 8 96 9 Year

Size Class (inches) 2004

Figure 5. Population estimates of small rainbow trout in the Hannon Memorial section of the Bitterroot River during the years indicated.

Bitterroot River-Hannon Memorial Rainbow Trout

2004

1000 96 90 500 89

0 89 90

10 11 96 12 13 14+ Year

Size Class (inches) 2004

Figure 6. Population estimates of large rainbow trout in the Hannon Memorial section of the Bitterroot River during the years indicated.

Bitterroot River Hamilton Rainbow Trout

2000

1500 2003

1000 2001 92 500

91 91

0 92 8 9 10

11 2001

2003 Year Size Class (inches)

Figure 7. Population estimates of small rainbow trout in the Hamilton section of the Bitterroot River during the years indicated.

Bitterroot River Hamilton Rainbow Trout

400 2003 300 200 2001 100 92

0 91

92 91 12 13 14 15 16+ 2001 Year 2003 Size Class (inches)

Figure 8. Population estimates of large rainbow trout in the Hannon Memorial section of the Bitterroot River during the years indicated.

10 Bitterroot River-Bell Crossing Rainbow Trout

2003 99 600 96 500 94 400 300 93 200 91 89

100 90

91 90 0 93 94

96 89

6 99 7 8 9 10 11 Year

Size Class (inches) 2003

Figure 9. Population estimates of small rainbow trout in the Bell Crossing section of the Bitterroot River during the years indicated.

Bitterroot River-Bell Crossing Rainbow Trout

2003 99 300 96 250 94 200 150 93 100 91 89

50 90

91 90

0 93 94

96 89

12 99 13 14 15 16 17+ Year

Size Class (inches) 2003

Figure 10. Population estimates of large rainbow trout in the Bell Crossing section of the Bitterroot River during the years indicated.

Bitterroot River-Stevensville Rainbow Trout

2004 2001 500 96 400 94 300 93 90 200 93 91 100 96 90 Year 0 2004 89 8 9 10 11 12 Size Class (inches)

Figure 11. Population estimates of small rainbow trout in the Stevensville section of the Bitterroot River during the years indicated.

Bitterroot River-Stevensville Rainbow Trout

2004 400 350 2001 300 250 96 200 94 150 90 100 93 93 50 96 0 91 2004 Year 13 14 15 16 17 18+ 90 Size Class (inches) 89

Figure 12. Population estimates of large rainbow trout in the Stevensville section of the Bitterroot River during the years indicated.

Brown Trout

Due to the time of year we collect population estimates spawning migrations have likely begun and this could bias our population estimates. Therefore, brown trout population estimates are more of an index than numeric estimate. Brown trout populations have remained stable in the study sections (Figures 13-22).

East Fork Bitterroot River 12.0 Brown Trout

2004

150 2003 2002 100 2001 50 2000 0 97 5 2000 6 7 8 9 10 11+ 2002 Year

Size Class (inches) 2004

Figure 13. Population estimate of brown trout in the East Fork Bitterroot 12.0 section during the years indicated.

The brown trout populations in the two East Fork Bitterroot sections has remained stable (Figure 13 and 14). Although rainbow trout numbers have declined in the lower East Fork, the brown trout numbers have not changed significantly. This would be consistent with other streams where whirling disease is having an impact.

In the Bitterroot River, our data indicate that brown trout populations have remained stable and possibly increased at Bell Crossing and Stevensville (Figure 15-22).

13 East Fork Bitterroot River 2.5 Brown Trout

2004 150 2003

100 2001 2000 50 98 0 98 6 7 8 9 10 11 12 13 14+ 2001

Size Class (inches) 2004 Year

Figure 14. Population estimate of brown trout in the East Fork Bitterroot 2.5 section during the years indicated.

Bitterroot River-Hannon Memorial Brown Trout

2004 400 96 300 90 200 89 100

0 89 90

8 96 9 10 11 12 Year Size Class (inches) 2004

Figure 15. Population estimate of small brown trout in the Hannon Memorial section of the Bitterroot River during the years indicated.

Bitterroot River-Hannon Memorial Brown Trout

2004 100 96 80 60 90 40 89 20

0 89 90

13 14 96 15 16 17 18+ Year Size Class (inches) 2004

Figure 16. Population estimate of large brown trout in the Hannon Mem orial section of the Bitterroot River during the years indicated.

15 Bitterroot River-Hamilton Brown Trout

150 2003 2001 100 92 50

0 92 7 8 9 10 11 2001 Year

Size Class (inches) 2003

Figure 17. Population estimate of small brown trout in the Hamilton section of the Bitterroot River during the years indicated.

Bitterroot River-Hamilton Brown Trout

300 2003

200 2001 92 100

0 92 12 13 14 15 16+

2001 Year

Size Class (inches) 2003

Figure 18. Population estimate of large brown trout in the Hamilton section of the Bitterroot River during the years indicated.

16 Bitterroot River-Bell Crossing Brown Trout

2003 99 200 96 150 94

100 93 89 91 50 93 96 89 0 2003 Year 7 8 9 10 11 Size Class (inches)

Figure 19. Population estimate of small brown trout in the Bell Crossing section of the Bitterroot River during the years indicated.

Bitterroot River-Bell Crossing Brown Trout

500 2003 400 99 300 96

200 89 94 100 93 96 93 0 2003 91 12 13 14 15 16 17 18+ Year 89 Size Class (inches)

Figure 20. Population estimate of large brown trout in the Bell Crossing section of the Bitterroot River during the years indicated.

Bitterroot River-Stevensville Brown Trout

2004 2001 200 96 150 93 100 91 50

89 89 91

0 93 96 8 9 10 11 12

2001 Year Size Class (inches) 2004

Figure 21. Population estimate of small brown trout in the Stevensville section of the Bitterroot River during the years indicated.

Bitterroot River-Stevensville Brown Trout

2004 2001 350 96 300 250 93 200 91 150 100 89 89

50 91 93

0 96 13 14 15 16+ Year 2001

Size Class (inches) 2004

Figure 22. Population estimate of large brown trout in the Stevensville section of the Bitterroot River during the years indicated.

18 Westslope cutthroat

The population estimates of westslope cutthroat indicate a stable population. The sections we were able to collect population estimates on are not the best sites for conclusive data. Specifically, the lower East Fork Bitterroot River only has recent data, the Bell Crossing and Stevensville sections support low populations and hybridization makes estimates difficult. We were unable to collect a westslope cutthroat population estimate on the Hamilton section and the Hannon section does not have enough historic data to identify a trend.

East Fork Bitterroot River 2.5 Cutthroat Trout

20 15 10 2004 5 0 2003 8 9 10 11 12 13+ 2003 Year 2004 Size Class (inches)

Figure 23. Population estimates of westslope cutthroat in the lower East Fork Bitterroot during the years indicated.

19 Bitterroot River-Hannon Memorial Cutthroat Trout

1000 2004 96 500

0 7 8 9 10 11 12 13 14+

Size Class (inches) 2004 Year

Figure 24. Population estimate of westslope cutthroat in Hannon Memorial section of the Bitterroot River during the years indicated.

Bitterroot River Bell Crossing Cutthroat Trout

16 2003 14 12 13 14 15 16+ 2003 Size Class (inches) Year

Figure 25. Population estimate of westslope cutthroat in the Bell Crossing section of the Bitterroot River during 2003.

20 Whirling Disease

Sampling fish for the presence of Myxobolus cerebralis was first undertaken in the Bitterroot River in 1995 (Clancy 2003). Since then, continuous sampling has occurred by Fish Wildlife and Parks personnel from Bozeman and region 2. We have used a combination of grab samples and sentinel cages to assess the presence and distribution of the parasite. Prior to 2000 we found that the parasite was present in the Bitterroot River and a few infected fish were found at scattered locations (Clancy and Javorsky 2001). Recent sampling has indicated that the upper Bitterroot River, and particularly the East Fork Bitterroot River, have high infection rates (Clancy 2003).. As previously reported in this document, the population of rainbow trout in the Conner area has declined significantly in the past two years and this may be due to the effects of whirling disease. The highest infection rates in the East Fork Bitterroot River have been found between Conner and Sula (Figure 26). These sites are also sites where high numbers of T. tubifex have been located. (Figure 27). These results are from Spring 2003 and 2004. Fall may be a better time to take samples in the Bitterroot system (E.R. Vincent, personal communication). But data from fall 2004 samples are not yet available.

Sentinel Cages

East Fork 2.5-Conner N 1.71-2.28

0.32-3.00

East Fork 12.0 0.54-2.37

Sula 0-0.02

Figure 26. Average infection rates of sentinel fish in cages set at various sites during Spring, 2003 and 2004.

21 T.Tubifex

East Fork 2.5-Conner Dickson –384 (3.65) N Spring Gulch 141 (2.13)

Braided Channels (0) Cameron Creek 7 (0) East Fork 12.0 Sula 1 (0) Sula Mink 25 (0)

Figure 27. The number of T.tubifex captured in qualitative sampling (visual prevalence of infection in parenthesis) at various sites in the East Fork Bitterroot drainage.

22 Radio Telemetry

During 2003, radio transmitters were implanted in 12 cutthroat trout in the Bitterroot River. The fish were captured between Bell Crossing and Florence and subsequently followed to learn which tributaries were used for spawning. A private contractor followed the fish from an airplane and FWP personnel helped from the ground. In past years, this method has been successful in identifying spawning tributaries (Clancy 2003). During 2003, we also picked up the signals of 5 fish from previous years. Of the 17 fish that were followed, only two ascended tributaries in 2003. One fish ascended Blodgett Creek and one fish ascended into Kootenai Creek.

None of the other fish left the Bitterroot River. Some made substantial migrations yet did not ascend tributaries and others made little or no migration. It is possible that some spawning takes place in the Bitterroot River. The 5 transmitters from past years were in fish of unknown status.

Skalkaho Creek ditches

Electrofishing in the ditches from Skalkaho Creek indicates that a significant number of fish are moving into the ditches during the irrigation season (Clancy 2003). Due to the complexity of the situation on Skalkaho Creek, a graduate project was initiated on Skalkaho Creek through Montana State University. Fishscreens that were installed and functional in 2004 were successful in screening many fish from 3 ditches. However, the status of those fish is still unknown (Gale and Zale 2005).

23 Bitterroot National Forest

During 2003 and 2004, we continued to monitor fish populations at established sites within the Bitterroot National Forest. Due to the widescale forest fires of 2000 and subsequent debris flows in some tributary streams, a graduate study was initiated to assess the impacts of the fires on native salmonids. Most of the study sites for the graduate study are duplicates of long term monitoring sites sampled previously by personnel from the Bitterroot National Forest or MFWP. I have not included the population estimates from that effort in this report. That data is being collected through Montana State University. The data from that study is being assimilated into our monitoring database.

The following discussion is for sites that were sampled by MFWP unless otherwise noted.

Darby District

The trends in cutthroat populations vary by site and it is not possible to characterize them on a district wide basis, partially due to impacts of the fires of 2000.

Daly Creek 0.7

The Daly Creek fish population was within the normal range from past estimates for both westslope cutthroat and bull trout.

Daly Creek 0.7 Cutthroat Trout

2003 2002 50 2001 40 30 99 N/1000' 20 89 10 84

85 85

0 89 99 84 4 5 6 7 8 9+ 2001

2002 Year

Size Class (inches) 2003

Figure 28. Population estimate of westlope cutthroat in the Daly Creek monitoring reach during the years indicated.

24 Daly Creek 0.7 Bull Trout

2003 2002 80 2001 60 99 N/1000' 40 89 20

85 85 89

0 99 5 6 7 2001 8 9+ Year 2002

Size Class (inches) 2003

Figure 29. Population estimates of bull trout in the Daly Creek monitoring reach during the years indicated.

Divide Creek 0.1

MSU collected this data that was within the normal range of past data.

Divide Creek 0.1 Cutthroat Trout

2003 2002 2001 80 96 60 91 N/1000' 40 90

20 89 90 89 91

0 96

4 2001 5 6 7+ Year 2002

Size Class (inches) 2003

Figure 30. Population estimates of westslope cutthroat trout in the Divide Creek monitoring reach during the years indicated.

Divide Creek 0.1 Bull Trout

2003 2002 350 2001 300 250 96 200 91 N/1000' 150 100 91

50 96 0

2001 Year 3 4 5+ 2002

Si z e Cla ss (inche s) 2003

Figure 31. Population estimates of bull trout in the Divide Creek monitoring reach during the years indicated.

North Fork Rye Creek 1.9

This section was impacted by the fires of 2000 and several subsequent debris torrents that caused significant fish mortality. However the population of westslope cutthroat has nearly recovered to pre-fire status, while the brook trout fishery has not. (Figures 32 and 33).

North Fork Rye Creek 1.9 Cutthroat Trout

2004 2003 2002 250 2000 200 97 150 N/1000' 96 100

89 91 50 90 91

96 90 97 0 89 3 4 2000 Year 5 6 7+ 2002 Size Class (inches) 2003 2004

Figure 32. Population estimates of westslope cutthroat trout in the N. Rye Creek monitoring reach during the years indicated.

30 Brook Trout 20

0 89 90 91 96 97 0 1 2 3 4 Figure 33. The number of brook trout captured during electrofishing in the North Rye Creek 1.7 section during the years indicated.

Rye Creek 6.6

This section of Rye Creek is just downstream of the mouth of North Rye Creek. Athe data was collected by personnel from the Bitterroot National Forest. The impacts of the fires on this population are unknown but most likely were not significant. The brook trout population has declined since the fires but the cutthroat population initially declined then stabilized (Figures 34 and 35). There may be a relationship between this section and North Rye Creek.

27 Rye Creek 6.6 Cutthroat Trout

2004

250 2003 200 2002 150 N/1000' 2001 100 50 0 2001

3 2002 4 5 6+ Year 2003

Size Class (inches) 2004

Figure 34. Population estimates of westslope cutthroat in the Rye Creek 6.6 section during the years indicated.

80 70 60 50 40 Brook Trout 30 20 10 0 1234

Figure 35. The number of brook trout captured during electrofishing in the Rye Creek 6.6 section during the years indicated.

28 Rye Creek 12.4

The native fishery of this reach was impacted significantly and possible permanently by the fires of 2000. Before the fires, the section was composed of westslope cutthroat and a small population of bull trout. Since the fire, bull trout have not been captured and increasing numbers of brook trout have been caught in this section. The westlope cutthroat population may have been impacted by the fires, but have recovered to historic levels since.

Rye Creek 12.4 Cutthroat Trout

2004 2003 2002

250 2001 2000 200 97 150 N/1000' 96

100 89

90 91 91

50 96 90 97

0 2000 89 2001

3 4 5 6+ 2002 Year 2003

Size Class (inches) 2004

Figure 36. Population estimates of westslope cutthroat trout in the Rye Creek 12.4 monitoring reach during the years indicated.

29 30

15 Bull Trout Brook trout 10

0 89 90 91 96 97 0 1 2 3 4

Figure 37. The number of bull trout and brook trout captured during electrofishing in the Rye Creek 12.4 section during the years indicated.

Skalkaho Creek 16.8 and 20.6

The number of large westslope cutthroat continues to increase since the catch and release regulations took effect (Figure 38). The bull trout population in this reach has remained fairly stable since sampling began in 1989 (Figure 39). The long term trend for both species is increasing numbers of larger fish. The upstream section data indicates similar trends (Figures 40 and 41).

30 Skalkaho Creek 16.8 Cutthroat Trout 2004 2003 2002 2001 2000 70 99 60 50 98 40 89 97 N/1000' 92 30 95 96 20 98 95 10 2001 Year 94 0 2004 4 5 93 6 7 8 9 10+ Size Class (inches) 92 91 90 89

Figure 38. Population estimates of westslope cutthroat trout in the Skalkaho Creek 16.8 monitoring reach during the years indicated

Skalkaho Creek 16.8 Bull Trout

2004 70 2003 60 2002 90 9291 50 93 2001 94 95 40 96 2000 97 N/1000' 98 30 99 99 2000 98 20 2001 Year 2002 97 10 2003 96 0 2004 95 5 6 7 8+ 94 Size Class (inches) 93 92 91 90 Figure 39. Population estimates of bull trout in the Skalkaho Creek 16.8 monitoring reach during the years indicated.

Skalkaho Creek 20.6 Cutthroat Trout 2003 2001 80 94 60 93 N/1000' 40 92 20 91

92 91 0 93 94 4 5 6 7 8+ Year 2001

Size Class (inches) 2003 Figure 40. Population estimates of westslope cutthroat trout in the Skalkaho Creek 20.6 monitoring reach during the years indicated

Skalkaho Creek 20.6 Bull Trout

2003 2001 94 200 93 150 92 N/1000' 100 91 91

50 92 93

0 94 Year 4 5 6+ 2001

Size Class (inches) 2003

Figure 41. Population estimates of bull trout in the Skalkaho Creek 20.6 monitoring reach during the years indicated.

32 Sleeping Child Creek 10.2

This monitoring section has been electrofished since 1989. The population of westslope cutthroat fluctuates annually, but was impacted seriously by debris flows in 2001 and 2002 (Figure 42). During 2002, no fish in the 4-5 inch range were captured, indicating that at least one year class of cutthroat trout was probably destroyed by the debris flows. The data from 2003 and 2004 indicate the population of westslope cutthroat is returning to pre-fire levels. The population of bull trout in this reach is small and difficult to enumerate.

Sleeping Child 10.2 Cutthroat Trout 2004 2003 2002 2001 2000 200 99 180 98 160 97 140 96 120 89 95 94 N/1000' 100 92 93 80 95 92 60 98 91 40 2001 Year 90 20 89 0 2004 86 4 5 6 7 8+ 85

Size Class (inches)

Figure 42. Population estimates of westslope cutthroat in the Sleeping Child 10.2 section during the years indicated.

Sula District

Some of the long-term monitoring reaches were sampled during 2003 and 2004. Most of the population estimates were within range of past data.

Bertie Lord Creek 0.2

The population of westslope cutthroat trout in this small stream has remained stable since sampling began in 1990 (Fig 43, 44). A small number of brook trout are also present, but most years not enough are captured to calculate a population estimate.

Bertie Lord Creek 0.2 Cutthroat Trout 2004 2003 2002 200 2001

150 99

N/1000' 100 91

90 90 50 91 99 0 2001

3 4 5 6+ 2002 Year 2003

Size Class (inches) 2004

Figure 43. Population estimates of westslope cutthroat in the Bertie Lord 0.2 section during the years indicated.

Bertie Lord Creek 0.2 Eastern Brook Trout

13 1999

N/1000' 12

11 4 5+ 1999 Year Size Class (inches)

Figure 44. Population estimates of brook trout in the Bertie Lord 0.2 section during the years indicated.

Camp Creek 2.3 (and 3.2)

This reach was restored from a ditch-like channel parallel to Highway 93 into a more natural meandering channel. The 1999 data represents a one-time population estimate

Camp Creek 2.3 and 3.2** Cutthroat Trout

2004 150 2003 100 N/1000' 1999** 50

0 2004 3 4 5 6 7 8 9+ Year

Size Class (inches)

Figure 45. Population estimates of westslope cutthroat in the Camp Creek sections during the years indicated.

35 before the restoration work. The 2003 and 2004 data represent the post-restoration data (Fig 45). The population of westslope cutthroat is similar in density since the work was completed, but due to the increase in stream length, the population of fish has increased. .

Martin Creek 1.3 and Moose Creek 1.4

The lower reaches of Martin and Moose Creeks support similar populations of westslope cutthroat (Figures 46, 47). The 2003 population estimates of westslope cutthroat was similar to past years. Both reaches support small numbers of bull trout, but population estimates were not collected in 2003 and 2004.

Martin Creek 1.3 Cutthroat Trout

2003 2002 100 2001 80 99 60 97 N/1000' 91 40 93 94 97 20 93 2001 Year 0 2003 92 4 5 6 7 8+ 91 Size Class (inches)

Figure 46. Population estimates of westslope cutthroat in the Martin Creek 1.3 section during the years indicated.

36 Moose Creek 1.4 Cutthroat Trout

2003 2002 150 2001

100 99 N/1000' 97 50 93 91 92 93

0 97 92 99 3 4 5 6 7 Year 91 8+ 2001

Size Class (inches) 2002 2003 Figure 47. Population estimates of westslope cutthroat in the Moose Creek 1.4 section during the years indicated.

Meadow Creek 5.6, Swift 0.7

This reach was first sampled in 1989. In 2003 and 2004 the population estimates of westslope cutthroat and bull trout are higher than past estimates (Figures 48-49). Swift Creek is a tributary of Meadow Creek. The fish population is stable (Fig. 50.51)

Meadow Creek 5.6 Cutthroat Trout 2004 2003 2002

200 2001 180 160 2000 140 96 120 N/1000' 100 95

80 89 90

60 91 94

40 94 95

20 96 91 0 2000 Year 90 4 2001 5 6 7 8+ 2002 2003 89 Size Class (inches) 2004

Figure 48. Population estimates of westslope cutthroat in the Meadow Creek 5.6 section during the years indicated.

37 Meadow Creek 5.6 Bull Trout

2003 2002 2000 200 96 150 95

N/1000' 100 94 89

90 90 50 94 95 89 96 0 Year 2000 4 5 6+ 2002

Size Class (inches) 2003 Figure 49. Population estimates of bull trout in the Meadow Creek 5.6 section during the years indicated.

Swift Creek 0.7 Cutthroat Trout

2003 100 2002 80 60 2001 N/1000' 40 95 20

0 95 4 5 6 7 8+ 2001 2002 Year Size Class (inches) 2003

Figure 50. Population estimates of westslope cutthroat in the Swift Creek 0.7 section during the years indicated.

38 Swift Creek 0.7 Bull Trout

2003 200 2002 150 2001 N/1000' 100 95 50

0 95

4 2001 5 6 7+ 2002 Year Size Class (inches) 2003 Figure 51. Population estimates of bull trout in the Swift Creek 0.7 section during the years indicated.

Warm Springs Creek 3.5

This reach of Warm Springs Creek was sampled in 2003 and 2004. The number of 6-8 inch fish was lower than in the past but overall the westslope cutthroat population was similar to past sampling, (Figure 52).

Warm Springs 3.5 Cutthroat Trout 2004 2003 150 2002 2001 100 N/1000' 2000 50 95 92 94

95 94 0 2000 92 4 5 6 7 2001 Year 8 9+ 2002 2003 Size Class (inches) 2004 Figure 52. Population estimates of westslope cutthroat in the Warm Springs 3.5 section during the years indicated.

39 Tolan Creek 5.1

This reach was first sampled in 1989. The Tolan Creek drainage burned in 2000, but the population of fish has remained stable (Figures 53, 54)

Tolan Creek 5.1 Cutthroat Trout 2004 2003 2002 2001 200 97 150 96 N/1000' 100 91 89

90 90 50 91 96

97 89 0 2001

4 5 6 7+ 2002 Year 2003 2004 Size Class (inches)

Figure 53. Population estimates of westslope cutthroat in the Tolan Creek 5.1 section during the years indicated.

Tolan Creek 5.1 Bull Trout

2004 2003 2002 2001 90 80 97 70 96 60 50 91 N/1000'

40 90

30 91 90 20 96 97 10

0 2001 Year 3 4 2002

5+ 2003 Size Class (inches) 2004

Figure 54. Population estimates of bull trout in the Tolan Creek 5.1 section during the years indicated.

40 West Fork District

Little West Fork1.3, Nez Perce 9.8

The population estimates were similar to past years in these sections (Figure 55, 56).

Little West Fork Creek 1.3 Cutthroat Trout

150 2004 100 1992 N/1000' 50

0 4 5 6 Year

7+ 1992 Size Class (inches) 2004 Figure 55. Population estimates of westslope cutthroat in the Little West Fork 1.3 section during the years indicated.

Nez Perce Fork 9.8

Nez Perce 9.8 Cutthroat Trout

2003 2002 200 2001 150 2000 N/1000' 100 92 50 92 0 Yea2000 r

4 2001 5 6 7+ 2002

Size Class (inches) 2003 Figure 56. Population estimates of westslope cutthroat in the Nez Perce 9.8 section during the years indicated.

41 Lake Como

Lake Como has been stocked annually with rainbow trout and more recently with kokanee. Each Fall we set gillnets to assess the status of the fishery. Trends in the data are probably not evident due to limited sampling (Table 1).

Table 1 . Capture of fish in 2 gillnets set overnight in Lake Como during the year indicated. Total number of each species is listed with the average length in parenthesis.

Year Rainbow trout Kokanee Largescale sucker 1998 4 (8.6) 61(8.7) 25(10.1) 1999 3(10.3) 15(7.8) 13(12.0) 2001 0 80(7.0) 30(8.5) 2002 8(10.5) 17(7.7) 33(8.4) 2003 3(9.6) 29(8.4) 16(9.8) 2004 5(11.6) 33(9.3) 6(8.0)

The stocking of kokanee did not occur in 2000 and 2002, did occur in 2003. The average size of kokanee was slightly higher in 2004.

42 LITERATURE CITED

Clancy, C.G. 1993. Statewide Fisheries Investigations. Bitterroot Forest Inventory. Project F-46-R-4. Montana Fish, Wildlife and Parks, Helena.

Clancy, C.G. 1996. Statewide Fisheries Investigations. Bitterroot Forest Inventory. Project F-46-R-4. Montana Fish, Wildlife and Parks, Helena.

Clancy, C.G. 1998. Statewide Fisheries Investigations. Bitterroot Forest Inventory. Project F-46-R-4. Montana Fish, Wildlife and Parks, Helena.

Clancy, C.G. 2003. Statewide Fisheries Investigations. Bitterroot River Drainage. Federal Aid Project No: F-113-R1, R2,R3. Montana Fish Wildlife and Parks, Helena

Gale, S. B., and A. V. Zale. 2005. Evaluation of entrainment losses of westslope cutthroat trout at private irrigation diversions and the efficiency of fish screens on Skalkaho Creek, Montana. Final Report to The Wild Fish Habitat Initiative, Montana University System Water Center, Bozeman, Montana. 75 pages.

Garn, H.S. and R.C. Malmgren. 1973. Soil and water resources of the Bitterroot National Forest, Montana. Part 1. USDA Forest Service. Bitterroot National Forest.

Gresswell, R.E. 1999. Fires and Aquatic Ecosystems in Forested Biomes of North America. Transactions of the American Fisheries Society 128:193-221.

Javorsky, L. 1994. The Bitterroot River floodplain: An historical analysis. Montana Department of Fish, Wildlife and Parks.

McFarland, R.C. 2004. Montana Statewide Angling Pressure 2003. Montana Department of Fish, Wildlife and Parks..

Montana Department of Fish, Wildlife and Parks. 1991. Bitterroot River Fisheries Management Plan for the period September 1991 to September 1996. Written by Joel Shouse Consulting Services, Bozeman, MT.

Nelson, M.L. 1999. Evaluation of the potential for resident bull trout to re-establish the migratory life form. M.S. Thesis. Montana State University, Bozeman.

Spoon, R.L. 1987. Evaluation of management of water releases for Painted Rocks Reservoir, Bitterroot River, Montana. Final Report. Montana Department of Fish, Wildlife and Parks. Bonneville Power Administration, contract report. Project 83-463, contract number DE-A179-83BP13076.

Prepared by: Christopher G. Clancy-June 2005

Stream Code Number Key Words Bitterroot River drainage 2-03-8865 Trout populations Whirling Disease Fishing regulations Westslope cutthroat Rainbow trout Brown trout Bull trout Brook trout Radio Telemetry Lake Como Bitterroot River Bitterroot National Forest