Upper Kootenay River Juvenile Bull Trout and Fish Habitat Monitoring Program: Summary

Transcription

1 Upper Kootenay River Juvenile Bull Trout and Fish Habitat Monitoring Program: Summary Prepared by: R.S. Cope Westslope Fisheries Ltd., 800 Summit Drive, Cranbrook, B.C., V1C 5J5 Prepared for: Herb Tepper B. C. Ministry of Environment Fisheries Branch, 205 Industrial Road G, Cranbrook, B.C., V1C 6H3 Funded by: Monitor and Protect Bull Trout for Koocanusa Reservoir BPA Project Number , Bonneville Power Administration, Fish and Wildlife Program P.O. Box 3621, Portland, OR 97208

2 Executive Summary This report compiles and summarizes the data contained in nine separate juvenile bull trout and fish habitat monitoring projects that make up the, Upper Kootenay juvenile bull trout (Salvelinus confluentus) and fish habitat-monitoring program ( ). This project is a co-operative initiative of the British Columbia Ministry of Environment (BCMOE) and Bonneville Power Administration (BPA), and comprises one component of the larger umbrella project, To monitor and protect upper Kootenay River bull trout (BPA Project Number ). The three study watersheds (Wigwam River, Skookumchuck Creek, White River) are considered the three most important bull trout spawning streams in the upper Kootenay River. Estimates of juvenile fish density (number of fish/100 m 2 ) were determined using closed, maximum-likelihood removal estimates for 13 index sites (e.g. reaches). Density estimates were completed for between 2 and 4 years at each site for a total of 42 density estimates over an 8- year time span (1997, ). In total, 2,411 bull trout fry and juveniles were captured over a total sample area of 20,724 m 2. Bull trout captures represented 84.3% of the catch. Site densities for bull trout fry and juveniles ranged from 0.4 to 45.5 fish/ 100 m 2. The Wigwam River had the highest mean annual fry and juvenile bull trout density estimates (range ), followed by the White River (range ), and the Skookumchuck River (range ). In total, 307 Westslope cutthroat trout were captured representing 10.7% of the catch. Westslope cutthroat trout were not the target species, but represent incidental captures, and as a result, densities were highly variable but typically low (range fish/100 m 2 ). Skookumchuck Creek had the highest mean annual Westslope cutthroat trout densities (range 0 9.2), followed by the Wigwam River (range ), and the White River (Range 0 0.2). The Level 1 Fish Habitat Assessment Procedure (FHAP) is a purposive field survey of current habitat conditions for the target species in select reaches. Regional criteria for habitat conditions do not exist and current diagnostic criteria to evaluate habitat condition are exclusive of bull trout and Westslope cutthroat trout data. This report provides watershed and site summaries of key FHAP habitat diagnostics data for the thirteen index sites. This data provides diagnostic criteria that can be utilized for standards to detect habitats that may be degraded or at risk within the Kootenay Region. While the data summarized are from watersheds that are far from being undisturbed watersheds, habitat data were derived from reaches of these watersheds that have been identified as regionally significant spawning and juvenile rearing habitat for bull i

3 trout, and to a lesser extent, Westslope cutthroat trout. Habitat data derived from these reaches identified preferred habitat features such as high habitat diversity, high large woody debris frequency, high value spawning and rearing substrate and groundwater sources. As a general rule, the generalized FHAP diagnostic ratings do a good job of classifying the index sites as high value bull trout and Westslope cutthroat trout habitat. However, they only rate as poor to fair in pool habitat and cover features using the generic diagnostics provided by Johnston and Slaney (1996). It would appear that this is due to several factors including; 1) the underlying character of the study streams that were much larger sized rivers compared to the diagnostics criteria, and 2) species and life-stage specific habitat preferences (e.g. small scour pools, cobble-boulder interstices). Juvenile bull trout in these watersheds prefer slightly higher gradient reaches (i.e %), that are slightly confined, have fewer pools (e.g. large, low velocity classically defined pools as opposed to boulder step-pools or small scour pools), and large substrate (i.e. cobble-boulder, dominant-sub-dominant) with a low percentage of sand and fines (i.e. clear interstices). These same habitat features (i.e. gradient, pool area, abundance of large woody debris (LWD) etc.) were not good predictors of fry densities. Westslope cutthroat trout densities and habitat diagnostic features were limited by the low abundance of cutthroat trout in the catch. Despite these limitations, Westslope cutthroat trout density was significantly related to pool area. Pool area and LWD frequency were correlated and juvenile Westslope cutthroat trout captures were typically associated with LWD. Stream classification of index sites was completed using the Rosgen Method (Rosgen 1996). This report provides tabular summaries of channel dimension, pattern and profile data from the reference reach data summary form, and the stream channel classification form. These quick reference summaries have been developed as a reference reach resource specific to the upper Kootenay watershed to assist in stream classification, assessment of impacts on stream potential and to develop restoration or compensation designs that match or accommodate the functioning of a streams natural stable tendencies. Eleven of the thirteen index sites were classified as Rosgen C3 and C4 streams. These stream reaches have gradients of 0 2 %, clean gravel and cobble substrate with very little sand or fines, high LWD abundance, wide floodplains with some off-channel habitat or side-channels and appear to be the dominant stream type for spawning, incubation and juvenile rearing bull trout and Westslope cutthroat trout. Channel bed morphology is riffle-pool, with regularly spaced ii

4 pools every 3 to 7 bankfull widths. Stream banks are dependent on riparian vegetation for stability. B3 channel types, with gradients of 2-4 % and very coarse substrate dominated by cobble and boulder material with very little sand or fines appear to be ideal habitat for bull trout and Westslope cutthroat trout juveniles. Channel bed morphology is dominated by a series of rapids and scour pools. Stream banks are composed of cobble and boulder and are very stable. Acknowledgements The upper Kootenay juvenile bull trout and fish habitat-monitoring program is a trans-boundary initiative implemented by the British Columbia Ministry of Environment (BCMOE), in cooperation with Bonneville Power Administration (BPA). Funding was provided by BPA under the umbrella project "Monitor and Protect Bull Trout for Koocanusa Reservoir", BPA project Number The contribution and assistance provided by Herb Tepper, Kevin Heidt and Bill Westover of the BCMOE are acknowledged and greatly appreciated. Suggested citation for this report: Cope, R.S Upper Kootenay Juvenile Bull Trout and Fish Habitat Monitoring Program: Summary. Prepared for the Ministry of Environment, Cranbrook, B.C. Prepared by Westslope Fisheries Ltd., Cranbrook, B.C. 46 pp + 2 app. Cover Photo Middlefork White River, Site 2. iii

5 Table of Contents EXECUTIVE SUMMARY... I ACKNOWLEDGEMENTS... III TABLE OF CONTENTS...IV LIST OF TABLES...V LIST OF FIGURES...VI 1 INTRODUCTION Background Project History Objective Study Area METHODS Juvenile Enumeration Fish Habitat Assessment RESULTS AND DISCUSSION Juvenile Fish Sampling Bull Trout Capture and Life-History Fry and Juvenile Densities Westslope Cutthroat Trout Capture and Life-History Densities Non-Target Species Fish habitat Assessment Fish Habitat Survey Bull Trout Density and Habitat Features Westslope Cutthroat Trout and Habitat Features Substrate Pebble Counts Rosgen Channel Surveys SUMMARY AND CONCLUSIONS REFERENCES Appendix A Fish Density Summaries Appendix B FHAP Level 1 Form 4 Summary Data iv

6 List of Tables Table 1. Characteristics of bull trout populations of the upper Kootenay River as summarized from data collected at enumeration fences. Note: Wigwam River data from Baxter and Westover (2000), Skookumchuck River data from Baxter and Baxter (2002), Gold Creek data from Cope and Morris (2005), White River data from Prince and Cope (2006) and Cope (2007)....7 Table 2. Schedule of program components for the upper Kootenay bull trout and fish habitat monitoring program, Table 3. Quick reference quide to permanent index site locations...16 Table 4. Total effort and catch for the upper Kootenay juvenile bull trout sample programs Table 5. Summary of mean fork length for three upper Kootenay juvenile bull trout populations Table 6. Summary of the mean annual fry and juvenile bull trout density estimates (fish/100m 2 ), by watershed Table 7. Summary of the mean fry and juvenile bull trout density estimates (fish/100 m 2 ) by site classification Table 8. Summary of mean fork length for incidental captures of Westslope cutthroat trout in three upper Kootenay bull trout streams...25 Table 9. Summary of the mean annual Westslope cutthroat trout juvenile density estimates (fish/100 m 2 ) by watershed Table 10. Summary of the Westslope cutthroat trout density estimates (fish/100 m 2 ) by site classification...27 Table 11. Diagnostics of habitat condition at the reach level for the three most important bull trout spawning and rearing tributaries to the upper Kootenay River (Wigwam, White and Skookumchuck Rivers) using the diagnostic ratings of Table 5 in Johnston and Slaney (1996). Note that the individual cell format represents value/rating A,B...30 Table 12. Proposed interim regional diagnostics criteria for habitat condition at the reach level for bull trout streams in the upper Kootenay using the diagnostic ratings of Table 5 in Johnston and Slaney (1996). Note that the individual cell format represents value/rating A,B...31 Table 13. Covariance values for select quantitative habitat diagnostic variables of habitat condition Table 14. Summary of substrate pebble count data for the Wigwam, White and Skookumchuck River index sites, Table 15. Quick reference summary of Rosgen (1996) channel dimension, pattern and profile data from the stream channel classification form...40 Table 16. Quick reference summary of a sub-set of the Rosgen (1996) channel dimension, pattern and profile data from the reference reach data summary form...40 v

7 List of Figures Figure 1. Kootenay basin study area... 2 Figure 2. Summary of annual bull trout redd surveys conducted on the three most important upper Kootenay River spawning tributaries identified using radiotelemetry... 4 Figure 3. Upper Kootenay River bull trout spawning streams... 6 Figure 4. Length frequency distribution and estimated age cohorts for juvenile bull trout populations. Note for presentation purposes scale interval changes from 5 mm to 10 mm at 70 mm Figure 5. Length-weight regression for fry and juvenile bull trout captured in the Skookumchuck, White and Wigwam Rivers, 1997 and Figure 6. Mean annual fry and juvenile bull trout density estimates (fish/100 m 2 ; +/- 95% Confidence Interval) for index sites within the three most important upper Kootenay River bull trout spawning tributaries Figure 7. Length frequency distribution and estimated age cohorts for incidental Westslope cutthroat trout captures Figure 8. Length-weight regression for incidental Westslope cutthroat trout captured in the Skookumchuck, White and Wigwam Rivers, 1997 and Figure 9. Mean annual Westslope cutthroat trout density estimates (fish/100 m 2 ; +/- 95% Confidence Interval) for index sites within the three most important upper Kootenay River bull trout spawning tributaries Figure 10. Regression of bull trout fry density versus pool frequency (mean pool spacing per bankfull channel width, W b ) Figure 11. Relationship between channel gradient and bull trout juvenile density in selected index sites in the Wigwam, White and Skookumchuck Rivers Figure 12. Relationship between pool frequency and bull trout juvenile density in selected index sites in the Wigwam, White and Skookumchuck Rivers Figure 13. Relationship between channel width and bull trout juvenile density in selected index sites in the Wigwam, White and Skookumchuck Rivers Figure 14. Relationship between pool area (%) and juvenile Westslope cutthroat trout density in selected index sites in the Wigwam, White and Skookumchuck Rivers Figure 15. Regression of bull trout fry versus the mean D 84 particle size Figure 16. Regression of bull trout juveniles versus the mean D 16 particle size vi

8 1 Introduction This report summarizes the results of the upper Kootenay juvenile bull trout (Salvelinus confluentus) and fish habitat monitoring projects completed in the Wigwam ( ), Skookumchuck ( ), and White Rivers ( ; Figure 1). These basins were selected as the three most important upper Kootenay River bull trout spawning tributaries, identified in an upper Kootenay River basin-wide radio telemetry project (Westover and Heidt 2004). The Wigwam, Skookumchuck, and White Rivers are three of the seven major streams and their tributaries, in the East Kootenay Region, that were designated as Class II Classified Waters in These streams support a regionally and internationally significant sport fishery with healthy populations of both bull trout and Westslope cutthroat trout (Oncorhynchus clarki lewisi). The classified waters of B.C. represent 42 highly productive trout streams. The classified waters licensing system was created to preserve the unique fishing opportunities provided by these waters, which contribute significantly to the province s reputation as a world class fishing destination. With funding from Bonneville Power Administration (BPA), the B.C. Ministry of Environment (BCMOE) has implemented a variety of projects designed to assess and monitor the status of wild, native stocks of bull trout in tributaries to Lake Koocanusa (Libby Reservoir) and the upper Kootenay River. The juvenile bull trout and fish habitat monitoring projects summarized in this report represent one component within the larger umbrella project, To monitor and protect upper Kootenay River Bull trout (BPA Project Number ). 1.1 Background Under the terms of the Columbia River Treaty between the United States and Canada, the U.S. Army Corps of Engineers built the Libby Dam on the Kootenay River, approximately 27 km upstream from Libby, Montana. The purpose of the dam was to provide hydroelectric power and flood control for the Kootenay and Columbia River basins. Construction began in 1969, impoundment was first achieved in March 1972, and the Libby Reservoir (known also as Lake Koocanusa) is 145 km long and spans the Canada-USA border between Montana and British Columbia. Lake Koocanusa reached full pool for the first time in July Average annual draw down on Lake Koocanusa 1

9 Figure 1. Kootenay basin study area. 2

10 exceeds 30 m and has ranged as deep as 52.4 m (Chisholm et. al. 1989). More recently, Lake Koocanusa water levels have also been manipulated for downstream Kootenay River sturgeon and salmon in the lower Columbia River, both of which are listed as threatened under the U.S. Endangered Species Act. Lake Koocanusa and the upper Kootenay River headwaters support a regionally and internationally significant meta-population of adfluvial bull trout. Bull trout populations have declined in many areas of their range within the Pacific Northwest including British Columbia. Bull trout were blue listed as vulnerable in British Columbia by the B.C. Conservation Data Center (Cannings 1993), and although there are many healthy populations of bull trout in the East Kootenay they remain a species of special concern. Bull trout in the United States portion of the Columbia River were listed as threatened in 1998 under the Endangered Species Act by the U.S. Fish and Wildlife Service. The upper Kootenay River watershed (above Libby Dam) is within the Kootenay subbasin of the Mountain Columbia Province, one of eleven eco-provinces that make up the Columbia River basin and has become a primary focus of research for bull trout in both Canada and the United States. Under the U.S. recovery plan for bull trout, Lake Koocanusa (and the Kootenay River watershed above Libby Dam) was considered a core area (USFWS 2002). Using this core area approach, recovery criteria require that at least 5 local populations with 100 or more individuals exist, and that the area should contain 1,000 or more adult bull trout. To achieve this requirement, population monitoring was required within this core area. In response to these concerns, the BCMOE applied for and received funding from BPA to assess and monitor the status of wild, native stocks of bull trout in tributaries to Lake Koocanusa and the upper Kootenay River (BPA Project Number ). 1.2 Project History Initially, emphasis was placed on determining abundance through downstream kelt fences and redd counts. The BCMOE in co-operation with the Montana Department of Fish, Wildlife and Parks (MDFWP), operated a fish fence and trap on the Wigwam River between 1996 and 1999 to enumerate and tag bull trout spawners (Baxter and Westover 2000). During this time, 3,287 bull trout were captured, many of which were repeat and alternate-year spawners. Over the four years, approximately 2,100 bull trout spawners 3

11 were floy and PIT tagged, 26 were radio tagged and another 10 sonic tagged. Radio telemetry studies have shown that these fish are part of an international population of bull trout that spend the winter in Lake Koocanusa in Montana and spawn in the Wigwam River in British Columbia. Bull trout redd counts have been conducted annually for the past 13 years in co-operation with MDFWP. These results indicated a significantly increasing population trend (Figure 2) Number of Redds Wigwam Skookumchuck White (Middle Fork) White (Blackfoot) Year Figure 2. Summary of annual bull trout redd surveys conducted on the three most important upper Kootenay River spawning tributaries identified using radiotelemetry. During the first five years of this project, eight additional tasks were undertaken to complement and expand on the Wigwam River bull trout studies. These were: 1) Skookumchuck Creek adult enumeration fence; 2) White River adult enumeration fence; 3) Gold Creek adult enumeration fence; 4) Wigwam River juvenile bull trout and fish habitat monitoring; 5) Skookumchuck Creek juvenile bull trout and fish habitat monitoring; 6) White River juvenile bull trout and fish habitat monitoring; 4

12 7) Upper Kootenay River bull trout radio telemetry; and 8) Five years ( ) of temperature data and substrate coring in known bull trout spawning areas has been collected (Tepper 2003). A total of 71 bull trout were surgically implanted with radio transmitters in the upper Kootenay River between April 1, 2000 and September 25, 2001 (Westover and Heidt 2004). These fish were tracked on a regular basis by both fix wing and helicopter for 2.5 years with the last flight occurring on September 16, The Wigwam River, a tributary to the upper Kootenay River in British Columbia, supports the majority of spawning bull trout from Lake Koocanusa. The upper Kootenay River spawning tributaries (e.g. upper Kootenay, Skookumchuck, White, Lussier, Bull, Palliser Rivers) demonstrated, to a lesser extent, similar overwintering migrations to Lake Koocanusa (Westover and Heidt 2004). Radio tagged bull trout were tracked into the Bull, Lussier, White, Skookumchuck and Verdant drainages. Approximately 35% of the radio tagged bull trout over-wintered below the full pool elevation of Lake Koocanusa, while the remaining 65% of the radio tagged bull trout over-wintered in the upper Kootenay River. As a direct result of the radio telemetry project three previously unknown bull trout spawning areas have been identified in the Middlefork White River, Blackfoot Creek, a tributary to the White River, and Verdant Creek (Figure 3). Although no radio tagged bull trout were tracked into the St. Mary River, snorkel observations by BCMOE staff have observed spawning bull trout and redds in Redding Creek, a tributary to the St. Mary River. BCMOE Fisheries staff confirmed another bull trout spawning area on Skookumchuck Creek, a tributary to the upper Kootenay River approximately 50 km north of Lake Koocanusa (Figure 3). A fence and trap were operated on Skookumchuck Creek for three years ( ) to capture out-migrating post spawning bull trout (Baxter and Baxter 2002). The use of the enumeration fence in the upper Kootenay River tributaries, over the past 10 years, has served as a valuable index of population size within the time frame of operation. This project has also provided an extensive database on the biological characteristics for four sub-populations within the upper Kootenay River core area (Table 1). 5

13 Middle Fork White River Upper Kootenay Juvenile Bull Trout Summary ( ) Vermilion River Verdant Creek N Simpson River Kootenay River W hite River Blackfoot Creek Skookum chuck C reek Lussier River Kootenay River Bull River Elk River Lake Koocanusa Wigwam River Kilometers Figure 3. Upper Kootenay River bull trout spawning streams 6

14 Table 1. Characteristics of bull trout populations of the upper Kootenay River as summarized from data collected at enumeration fences. Note: Wigwam River data from Baxter and Westover (2000), Skookumchuck River data from Baxter and Baxter (2002), Gold Creek data from Cope and Morris (2005), White River data from Prince and Cope (2006) and Cope (2007). Wigwam (731 km 2 ) Skookumchuck (641 km 2 ) Gold Cr. (816 km 2 ) White (987 km 2 ) N. White (223 km 2 ) Variable Total Bull Trout (fence) Bull Trout count (snorkel) b 119 n/a n/a n/a n/a n/a 123 n/a n/a Females : Males 1.9:1 2.5:1 2.5:1 2.2:1 3.0:1 2.8:1 1.6:1 1:1 1.6:1 2.9:1 2.2:1 Total Redds Enumerated n/a Bull Trout/Redd (est.) n/a 3.8 a 2.7 a n/a Total Length (cm) Mean Range Male Length (cm) Mean Range Female Length (cm) Mean Range Timing Through Fence Peak Sept 30 Oct 1 Sept 24 Sept20 Sept 20 Sept 19 Sept 26 Sept 20 Sept 24 Sept 23 Sept 16 Start Sept 11 Sept 13 Sept 9 Sept 9 Sept 7 Sept 6 Sept 7 Sept 15 Sept 9 Sept 7 Sept 1 End Oct 14 Oct 14 Oct 14 Oct 14 Oct 16 Oct 12 Oct 10 Oct 18 Oct 9 Oct 1 b 27 Sept a note that the number of bull trout per redd was based on redds in index sites only and is known to be high for this system. Index Sites for the White River encompass a much lower proportion of the known spawning habitat as compared to the Wigwam and Skookumchuck. b note that a rain on snow event removed the fence prematurely and fish were still emigrating. 7

15 A total of 834 bull trout were passed through the Skookumchuck fence during the three years of operation and another 127 bull trout were holding in a pool immediately above the fence when it was removed during mid-october (Table 1). The 2002 out-migrants totalled 309 bull trout and were comprised of 28 (9.1%) repeat spawners from 2001, 25 (8.1%) alternate year spawners from 2000 and 6 (1.9%) double repeat spawners from 2000 and Pelvic fin rays were collected from a size range of 41 bull trout for ageing with ages ranging from 5 to 14 years old. Seven bull trout had floy tags present from sampling in the lower Bull River between 1997 and 2001 (Baxter and Baxter 2002). A fence and trap were operated on the White River, near its confluence with the Kootenay River, for two years (2003 and 2005), to capture out-migrating bull trout (Prince and Cope 2006). A total of 1,428 bull trout were passed through the fence during the two years of operation (Table 1). In addition, another 123 bull trout were holding in the pools immediately above the fence when it was removed during mid October. In 2005, outmigrants totalled 652 before the fence was breached; of these 137 or 21% also spawned in There were thirteen recaptures from previous bull trout tagging programs within the upper Kootenay watershed. Five bull trout were previously tagged in the Bull River, seven were tagged in the Kootenay River and one was tagged in the White River. Nine of these recaptures were originally tagged in 2000 for the upper Kootenay River radio telemetry project. In 2004, a fence and trap were operated on Gold Creek, a smaller tributary stream to Lake Koocanusa, immediately north of the Canada-United States border. Gold Creek was a system with known bull trout use, but the extent of use was only anecdotal. A total of 61 bull trout kelts were captured, of which there were no previously tagged bull trout (Cope and Morris 2005; Table 1). In 2006, the fence and trap were operated on the North White River, one of three forks that represent the upper White River (Cope 2007). The North White River was another tributary with known bull trout use, but the extent of use was only anecdotal. A total of 119 downstream kelts were passed through the fence. Juvenile bull trout and fish habitat monitoring was undertaken at six permanent index sites in the Wigwam River and Bighorn Creek ( ), four permanent reference sites in Skookumchuck and Sandown Creeks ( ), and three permanent reference sites in the Middlefork White River and Blackfoot Creek ( ). 8

16 At each permanent index site (n=13), over three consecutive years, juvenile bull trout and where possible, Westslope cutthroat trout densities, stream habitat conditions (Resource Inventory Committee (RIC) approved Fish Habitat Assessment Procedures (FHAP), Level 1, Form 4; Johnston and Slaney (1996)), and detailed geomorphic surveys (Rosgen 1996) were documented over two stream meander wavelengths. The objective of this project was to develop a better understanding of inter-annual variation in juvenile bull trout and Westslope cutthroat trout recruitment and the ongoing hydrologic and morphologic processes in their major spawning and early rearing streams in the upper Kootenay River, especially as they relate to spawning and rearing habitat quality. 1.3 Objective This report summarizes the results of the nine upper Kootenay juvenile bull trout and fish habitat monitoring projects completed within the Wigwam, Skookumchuck and White watersheds between 2000 and 2005, inclusive. This report compiles and summarizes the databases for fry and juvenile bull trout and Westslope cutthroat trout density estimates and compares these to select salmonid habitat condition diagnostics for these same permanent index sites. The objective of this report was three-fold: 1. Compile the juvenile catch and density data and the fish habitat assessment data from the nine individual juvenile bull trout projects into single databases; 2. Compare and contrast the density data and fish habitat data to assist in the development of regional diagnostics of salmonid habitat specific to juvenile bull trout (i.e. Johnston and Slaney 1996). 3. Where possible, compare and contrast Westslope cutthroat trout densities and habitat conditions. The following list outlines the nine individual juvenile bull trout and fish habitat monitoring projects summarized in this report: Cope, R.S Middlefork White River and Blackfoot Creek juvenile bull trout and fish habitat monitoring program: 2005 data report. Prepared for the British Columbia Ministry of Environment, Cranbrook, B.C. Prepared by Westslope Fisheries Ltd., Cranbrook, B.C. 34 pp + 7 app. 9

17 Cope, R.S. and K.J. Morris Middlefork White River and Blackfoot Creek juvenile bull trout and fish habitat monitoring program: 2004 data report. Prepared for the British Columbia Ministry of Land, Water, and Air Protection, Cranbrook, B.C. Prepared by Westslope Fisheries Ltd., Cranbrook, B.C. 32 pp + 7 app. Cope, R.S. and K. Morris Skookumchuck Creek juvenile bull trout and fish habitat monitoring program: 2004 data report. Prepared for the British Columbia Ministry of Land, Water, and Air Protection, Cranbrook, B.C. Prepared by Westslope Fisheries Ltd., Cranbrook, B.C. 40 pp + 7 app. Cope, R.S Middlefork White River and Blackfoot Creek juvenile bull trout and fish habitat monitoring program: 2003 data report. Prepared for the British Columbia Ministry of Land, Water, and Air Protection, Cranbrook, B.C. Prepared by Westslope Fisheries Ltd., Cranbrook, B.C. 29 pp + 7 app. Cope, R.S Skookumchuck Creek juvenile bull trout and fish habitat monitoring program: 2003 data report. Prepared for the British Columbia Ministry of Land, Water, and Air Protection, Cranbrook, B.C. Prepared by Westslope Fisheries Ltd., Cranbrook, B.C. 40 pp + 7 app. Cope, R.S Skookumchuck Creek juvenile bull trout and fish habitat monitoring program: 2002 data report. Prepared for the British Columbia Ministry of Land, Water, and Air Protection, Cranbrook, B.C. Prepared by Westslope Fisheries Ltd., Cranbrook, B.C. 28 pp + 7 app. Cope, R.S Wigwam River juvenile bull trout and fish habitat monitoring program: 2002 data report. Prepared for the British Columbia Ministry of Land, Water, and Air Protection, Cranbrook, B.C. Prepared by Westslope Fisheries, Cranbrook, B.C. 35 pp + 5 app. Cope, R.S., K. Morris and J.E. Bisset Wigwam River juvenile bull trout and fish habitat monitoring program: 2001 data report. Prepared for the British Columbia Ministry of Land, Water, and Air Protection, Cranbrook, B.C. Prepared by Westslope Fisheries, Cranbrook, B.C. 28 pp + 5 app. Cope, R.S. and K. Morris Wigwam River juvenile bull trout and fish habitat monitoring program: 2000 data report. Prepared for the British Columbia Ministry of Environment, Lands and Parks, Fisheries Branch, Cranbrook, B.C. Prepared by Westslope Fisheries, Cranbrook, B.C. 33 pp + 4 app. In addition, the Wigwam River project represented a sub-set of the index sites originally established in the preliminary Wigwam River project identified below. Catch and density data from this project were included in this data summary. Cope, R.S Wigwam River fish forestry study: preliminary surveys (1997). Prepared for the British Columbia Ministry of Environment, Lands and Parks, Kootenay Region, Nelson, B.C. Prepared by Interior Reforestation Co. Ltd., Cranbrook, B.C. 53 pp + 4 app. 10

18 1.4 Study Area The three upper Kootenay River bull trout spawning and rearing tributaries representing the upper Kootenay juvenile bull trout and fish habitat monitoring program are illustrated in Figure 1. The Wigwam, Skookumchuck and upper White River are described in detail within each of the annual reports. These watersheds are considered the three most important bull trout spawning tributaries in the upper Kootenay River basin. Specific index sites are illustrated in geo-referenced 1:50,000 TRIM maps included within each report. Typically, permanent index sites were selected to include contrast within each watershed. At a minimum, one preferred bull trout spawning reach, one low density bull trout spawning reach and one smaller spawning and rearing tributary were included within each watershed. Typically, the low-density sites were located in the lower reaches of the watersheds and the preferred spawning reaches and rearing tributaries were located in the upper reaches of the watersheds. 2 Methods Index sites were a minimum of 20 channel widths in length or a distance equal to two stream meander wavelengths. At each site, the following reference points were permanently established, geo-referenced (UTM) and marked with a combination of metal tree tag, tree blaze, fluorescent tree paint, and flagging tape: 1) Upstream and downstream elevation benchmarks (benchmarks were a lag bolt embedded in the base of a large, stable, riparian tree). 2) Upstream and downstream limits of the longitudinal survey. 3) Riffle and pool cross-sectional benchmarks (lag bolt embedded in the base of a riparian tree) and re-bar bank pins representing the start and finish reference points. 4) Electrofishing habitat units. 2.1 Juvenile Enumeration Estimates of juvenile fish density (number of fish/100 m 2 ) were determined using closed, maximum-likelihood removal estimates (Riley and Fausch 1992). For each site, three habitat units (riffle, pool and glide) were individually sampled for fish densities over a combined total of approximately 400 to 500 m 2. This methodology allows for habitat unit comparisons as well as reach comparisons through pooling of habitat units to obtain a 11

19 mean. A Smith-Root Mark 12POW backpack electro-shocker was used for successive depletions within each closed sample unit. Although bull trout are the main focus of this project, densities of Westslope cutthroat trout are also reported. Catch results from the three habitat units within each index site were summed, by pass. These results were then used to estimate the number of fry (0 + age class) and juveniles (1 + and 2 + age classes) within the composite enclosure area. Population estimates were calculated using the Microfish software package (Van Deventer and Platts 1990). Population estimates and their 95% confidence interval were then reported as a standard numerical density for each site (number fish/100 m 2 ). Capture, effort and life history data were input using the BCMOE Microsoft Access tool, Fisheries Data Information Summary System (FDIS). Data from each of the nine annual projects were exported from FDIS into Microsoft Excel export files for each project. These nine files were then collated into the single Microsoft Excel File UKBT Density data.xls. This file contains all effort, catch, and density estimates by index site, site type, watershed and year. The corresponding life-history information for these fish was compiled into the Microsoft Excel File UKBT Individual fish data.xls. 2.2 Fish Habitat Assessment Using the RIC approved FHAP, Level 1, Form 4 - Habitat Survey Data Form (Johnston and Slaney 1996), a standard suite of habitat parameters were collected for each habitat unit within the length of the index site (minimum of 20 channel widths in length or a distance equal to two stream meander wavelengths). The level 1 FHAP is a purposive field survey of current habitat conditions for the target species in select reaches. This form has been developed for interpretation of habitat sensitivity and capability for fish production and includes prominent physical features such as pool and riffle ratios, residual pool depths, channel stability, flood indicators, cover components, abundance of large woody debris (LWD) and riparian vegetation. FHAP data for each project was input using the BCMOE Microsoft Access Tool Watershed Restoration Program Data Summary System. Each completed project was then exported and the nine datasets were compiled in the Microsoft Excel File UKBT Summarized FHAP Data.xls. As these surveys were replicated at each site for three consecutive years, the 12

20 final year of each assessment was compiled and summarized in the Microsoft Excel file UKBT FHAP Table 5.xls. Stream classification of index sites was completed using the Rosgen Method (Rosgen 1996). The following measurements of channel profile, pattern and dimension were completed to facilitate channel classification: 1) A longitudinal profile (minimum of 20 channel widths in length or a distance equal to two stream meander wavelengths) of the stream bed following the thalweg of the stream channel including measurement of water surface (slope) and bankfull elevations. 2) Stream cross-sections on both a riffle and pool segment (stream bed, water surface, thalweg and bankfull elevations). 3) Channel pattern (width flood prone area, sinuosity, belt width, meander length and radius of curvature). 4) Modified Wolman pebble count (reach and active channel at a riffle). At a maximum of 10 m intervals, following the thalweg of the stream channel, the elevation of the streambed and the water surface was surveyed over the length of the study area. All stream and habitat unit gradients were calculated from differences in water surface elevation. Cross sectional profiles were surveyed at 1 m intervals and extended 5 m beyond the bankfull width. The elevation of the bankfull channel was also noted at each cross section location and periodically throughout the longitudinal survey. Geomorphic surveys were completed using an auto level (Topcon AT-G7 Auto Level) and standard differential hydrometric survey techniques (Anon. 1998). A differential loop was used to accurately determine benchmark elevations, express error terms and ensure quality control. Characterization of channel bed material employed the modified Wolman method outlined in Rosgen (1996). Briefly, this procedure uses a stratified, systematic sampling method based on the frequency of riffle/pools and step/pools occurring within a channel reach that is approximately bankfull channel widths in length (or two meander wavelengths). The modified method adjusts the material sampling locations so that various bed features are sampled on a proportional basis along a given stream reach. In total, 10 transects are 13

21 established and 10 substrate particles are selected at systematic intervals across the bankfull channel width, for a total sample size of 100. To avoid potential bias, the actual particle was selected on the first blind touch, rather than visually selected. The intermediate axis of the particle was measured such that the particle size selected would be retained or pass a standard sieve of fixed opening. The composite particle distribution was used to represent the reach. A second modified Wolman pebble count was completed within the active channel (i.e. within the wetted width), at the representative riffle cross-section, to calculate D 84. The D 84 estimate was then used to estimate a roughness coefficient in velocity calculations. Initially, in the Wigwam River, Rosgen channel survey data and channel classification data for each index site was input using Microsoft excel spreadsheets. Beginning with the Skookumchuck Project, Rosgen channel surveys were input using the Microsoft Excel tool, The Reference Reach Spreadsheet, Version 2.4 L SI, (River4m Ltd. and D. Mecklenburg 1999). This spreadsheet and summary system was developed and distributed by the Ohio Department of Natural Resources as a stream channel assessment tool, forms, calculators and a format for data management. Summary data from this spreadsheet was then input into the Microsoft Excel Worksheet Rosgen Level II Forms, that contain a Reference Reach Data Summary, and a Stream Classification Form, for each index site. Summary reference reach data and classification data for each index site were then compiled in the Microsoft Excel file, UKBT Rosgen Reference Reach Data.xls. Pebble count summary data for mean size of sediment particles less than six percent categories ( D 16, D 35, D 50, D 65, D 84, D 95 ) was compiled in the Microsoft Excel file, UKBT Pebble Count Summary.xls. Stream discharge was estimated at each electrofishing location using a Price 1210AA velocity meter and wading rod calibrated bi-annually by the National Calibration Service of the National Water research Institute. 14

22 3 Results and Discussion The sampling schedule for the juvenile bull trout fish habitat monitoring program is summarized in Table 2. To ensure consistency among watersheds and years, every effort was made to ensure the fish sampling was completed within the first two weeks of August. The first two weeks of August were considered the ideal timing for targeting bull trout and Westslope cutthroat trout fry. The FHAP and channel surveys were not considered as critical in terms of timing. These surveys were completed opportunistically later in the fall. Table 2. Schedule of program components for the upper Kootenay bull trout and fish habitat monitoring program, Program Component Watershed Juvenile Fish Sampling Wigwam Aug Aug Aug Aug Skookumchuck Aug Aug Aug White Aug Aug Aug FHAP and Channel Surveys Wigwam Sep 20-Oct 04 Sep 14-Oct 05 Aug 26- Sep 19 Skookumchuck Sep 22- Oct 01 Aug 12- Sep 26 Sep 10-Oct 27 White Sep 18 Oct 01 Sep 27 Oct 14 Aug 17 Sep 18 Table 3 provides a quick reference summary of the locations, co-ordinates (upstream limit of the two meanders) and site classifications for the 13 permanent index sites summarized in this report. 15

23 Table 3. Quick reference quide to permanent index site locations. Watershed Sub-basin Site No. 2 Sample Years Location Description UTM 1 (Zone.Easting.Northing) Site Classification Wigwam Wigwam , Wigwam Wigwam , Wigwam Wigwam , Wigwam Wigwam , Wigwam Bighorn , Reach 5 immediately d/s Bighorn Creek Confluence Reach 6 immediately d/s of the Rocky Mountain Lodge Reach 7 immediately u/s of Brewery Creek Reach 9 immediately at the Rabbit Creek Confluence Reach 1 immediately u/s of the bridge at Forest Rec. Site. Wigwam Wigwam , 2002 Reach 2 immediately d/s of Lodgepole Creek Skookumchuck Skookumchuck Pulp Mill site immediately d/s of Skookumchuck River bridge. Skookumchuck Skookumchuck U/s Skookumchuck FSR 3 km 38. Skookumchuck Skookumchuck Skookumchuck FSR km 42 spur road. Skookumchuck Sandown Sandown Creek upstream of FSR Bridge Preferred BT Spawning Preferred BT Spawning Preferred BT Spawning Low Density Spawning Tributary Spawning/Rearing Low Density Spawning Low Density Spawning Preferred BT Spawning Preferred BT Spawning Tributary Spawning/Rearing White Middlefork Axel FSR km Preferred BT Spawning White Middlefork Middlefork FSR km Preferred BT Spawning White Blackfoot Blackfoot FSR km Tributary Spawning/Rearing 1 Note that the co-ordinates provided represent the upstream limit of the two meander lengths of the index site. Additional co-ordinates for the downstream limit, stream cross-sections, benchmarks and electrofishing sites can be found in the individual reports. 2 Refer to Table A1 (Appendix A) for reference to the 1997 site numbers that were used for trend analyses with the current program. 3 FSR = Forest Service Road. 16

24 3.1 Juvenile Fish Sampling A total of 2,859 fish were captured in the upper Kootenay juvenile bull trout and fish habitat monitoring project (Table 4). A total of 20,724 m 2 or 2.07 ha of fish habitat was sampled within the three most important bull trout spawning and rearing tributaries to the upper Kootenay River (Table 4). Table 4 includes comparative data from the preliminary survey conducted in the Wigwam River in The 1997 data was included because of its applicability. The Wigwam River sampling replicated a sub-set of the 1997 index sites using the same personnel and equipment, with no or only minor adjustments to the electrofishing sites. Table 4. Total effort and catch for the upper Kootenay juvenile bull trout sample programs. Watershed Year Electrofishing Effort (sec.) Sample Area (m 2 ) No. of Sites BT Catch WCT Catch Incide ntal Catch Total Catch White ,654 1, ,871 1, ,471 1, Skookumchuck ,916 1, a 35,585 1, a 33,705 1, Wigwam 1997 b,c 41,008 2, ,454 2, ,450 2, b 49,507 3, Total 332,621 20, , ,859 a total includes additional site at Sandown Creek b total includes site in lower Wigwam (d/s of Lodgepole). C Appendix A contains a cross-reference index relating the 1997 index site numbers used in the comparison with the current program. 17

25 3.1.1 Bull Trout Capture and Life-History A total of 2,411 bull trout fry and juveniles were captured in this monitoring program (Table 4). Bull trout represent 84.3% of the catch within the study streams. Based on capture observations over the course of this program and a qualitative review of the lengthfrequency data, the upper fork length limit of fry during the sample period of early to mid August was assumed to be 70 mm. Based on this assumption, bull trout fry (n=2,164) represented 89.8% of the total bull trout catch. This predominance of bull trout fry in the catch was expected. Bull trout fry were the target species and life stage and as such, the catch composition reflects bias associated with site selection for this capture target. In addition, all sample sites were derived from watersheds that have been characterized as the most important bull trout spawning streams in the Kootenay Region. Fry and juvenile bull trout captures ranged in fork length from 24 mm to 208 mm (n=2,411). Figure 4 presents the length frequency data by watershed. The modal class, in 5 mm intervals was mm (Skookumchuck and White) and mm (Wigwam River). This size class represents the young-of-the-year cohort (fry, 0 + ). Mean fork lengths of each age class estimate are summarized for each watershed in Table 5. The growth rate of fry and juvenile bull trout in the Skookumchuck, Wigwam and White Rivers for the period 1997 and combined was described by the equation: Log 10 Weight = Log 10 Length (Figure 5). 18

26 Wigwam Frequency Skookumchuck More Frequency Frequency More White More Length (mm) Figure 4. Length frequency distribution and estimated age cohorts for juvenile bull trout populations. Note for presentation purposes scale interval changes from 5 mm to 10 mm at 70 mm. 19

27 Table 5. Summary of mean fork length for three upper Kootenay juvenile bull trout populations. Age Wigwam Skookumchuck White YOY (20-70mm) Mean SE n Range (71-140mm) Mean SE n Range ( mm) Mean SE n Range Log 10 Weight = Log 10 Length r 2 = n = 2, Log Weight (g) Log Fork Length (mm) Figure 5. Length-weight regression for fry and juvenile bull trout captured in the Skookumchuck, White and Wigwam Rivers, 1997 and

28 Fry and Juvenile Densities In total, 42 densities were estimated over an 8-year time span for 13 index sites (e.g. reaches). Table A2 (Appendix A) provides a summary of the 42 density estimates and their confidence limits for bull trout fry, bull trout juveniles, and fry and juveniles combined. Site densities for bull trout were characterized by variability and ranged from 0.4 to 45.5 fish/100 m 2 (fry and juveniles combined; Table A2). The mean annual density estimates for each watershed, are presented in Figure 6. The mean 2002 fry density in the Wigwam River was the lowest estimated density for the Wigwam enumeration program (Figure 6), even though enumeration of bull trout redds was the highest on record, to date (Figure 2). This 2002 decrease was hypothesized to be due to a drought-induced shift in spawning distribution, not a decrease in fry survival. A drought cycle in the hydrograph began in 2000, and became particularly significant in the fall of 2001 (Prince and Morris 2003). During the fall 2001 spawning season, water levels within the upper Wigwam River were extremely low and in fact, surficial flow was absent in much of reach 7 for most of August and September. This limited accessibility caused a distribution shift to increased spawning at lower river locations (reaches two and five in particular). Trends in fry abundance are related to proximity to spawning areas and the shift in redd distribution was subsequently reflected in 2002 juvenile density sampling. Therefore, total bull trout fry production may not have been impacted as the mean density might suggest as the decrease in densities at the upper index sites may have been more than compensated for by an increase in densities in the lower reaches. The Wigwam River typically had the highest mean annual fry and juvenile bull trout density estimates, followed by the White, and Skookumchuck Rivers (Table 6). Watershed trends in fry and juvenile densities were similar to trends in the estimated size of the spawning population within these respective watersheds (Table 1). Table 6. Summary of the mean annual fry and juvenile bull trout density estimates (fish/100m 2 ), by watershed. Fry Juveniles Fry and Juv. Combined Watershed N Mean Range Mean Range Mean Range Wigwam White Skookumchuck