Project Title
Statement of Work and Budget FY2005

BPA Project Number:  1988065-00
BPA Project Title: Kootenai River Fisheries Recovery Investigations
Contract Number:  00004691
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Vaughn L. Paragamian
Principal Fisheries Research Biologist
Idaho Department of Fish and Game
2750 Kathleen Ave.
Coeur d' Alene, Idaho  83815
(208) 769-1414  (208) 769-1418
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Conan Chiu
Contracting Officer
Idaho Department of Fish and Game
1075 Park Blvd, P.O. Box 25
Boise, Idaho 83707
(208) 287-2813 / (208) 334-2148Fax
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The Kootenai River Fisheries Recovery Investigations is comprised of four projects or studies; white sturgeon monitoring and evaluation and recovery actions, burbot investigations and rehabilitation, salmonid studies and rehabilitation, and ecosystem rehabilitation.  

The Kootenai River White Sturgeon Project (Project 88-65) began September 1, 1988.  Through a cooperative effort IDFG and KTOI completed an assessment of the status of white sturgeon in the Kootenai River, successfully cultured sturgeon from the endemic stock, and stocked age-1 and age-2 sturgeon into the Kootenai River on an experimental basis (Apperson and Anders 1990 and 1991; Apperson 1992).  Recruitment of wild sturgeon to the Kootenai River population has been very limited since Libby Dam began operation in 1972.  Regulated flow from the dam has been identified as the primary factor limiting sturgeon spawning (Partridge 1983) and spawning location may be limiting egg survival and early rearing (Paragamian et al. 2001; Paragamian et al. 2002).  On June 11, 1992 this population was petitioned for protection under the Endangered Species Act (ESA).  As a result of the petition, an agreement was developed between the U. S. Army Corps of Engineers (USACE) and USFWS to alter operation of Libby Dam to enhance sturgeon recruitment.  In September of 1994 the Kootenai River white sturgeon was listed as an endangered species.  A multi agency international recovery team was formed to develop and implement a recover plan.  The Kootenai River White Sturgeon Recovery Team (KRWSRT) was formed and in 1999 a Kootenai River White Sturgeon Recovery Plan (KRWSRP) was approved (USFWS 1999).  Many of the white sturgeon studies in this document follow the guidelines and study measures established in the KRWSRP.  


Increased flows during spring when white sturgeon spawn was an important measure within the white sturgeon Recovery Plan.  Monitoring and evaluation of the spawning by white sturgeon during these flows is an important task of the IDFG.  White sturgeon spawning events during the years 1994 through 2000 were compared to daily average flow and daily average temperature at Bonners Ferry for each event (Paragamian and Wakkinen 2002).  White sturgeon often spawned during decreasing flows, the number of events each year ranged from as few as nine to as many as 20, with the number of days during the  spawning period ranging from 17 to 31 d. The most consistent year of Kootenai River white sturgeon spawning was 1996 when  spawning was detected during 18 of 19 days.  In 1996 flow ranged from 891 to 1,259 m3/s (31,465-44,461 cfs) and averaged about 1,131 m3/s (~40,000 cfs) for the first 11 events before there was a day of undocumented spawning.   Average daily temperature during spawning ranged from 7.5 to 14oC (45.5-57.2 oF), with the highest probability of spawning (48%) at the 9.5-9.9oC (49.1-49.9oF) range (Paragamian and Wakkinen 2002).
  
Flow was an important variable affecting sturgeon spawning.  Average daily flow for spawning events from 1994 through 2000 ranged from 141 to 1,265 m3/s (4,979-44,673 cfs) but most (63%) spawning took place above 630 m3/s (22,248 cfs) (Paragamian and Wakkinen 2002).   Analysis suggests flows for optimum white sturgeon spawning in the Kootenai River should be held above 630 m3/s (22,248 cfs) but ideal flows would be at about 1,131 m3/s (~40,000 cfs) or more if structural damage was not inevitable, an ideal temperature range of 9.5 to 12oC (49.1-53.6 oF), and a duration of 42 d which is based on recommendations in the Kootenai River White Sturgeon Recovery Plan (USFWS 1999).  However, of the two variables (temperature and flow) temperature is the most difficult to control.

There is mounting concern that more than flow mitigation may be necessary to recover this population of white sturgeon.  White sturgeon in the Kootenai River continue to spawn over sand substrate, which is thought to be unsuitable for adequate survival of eggs and larvae.  Recent evidence suggests white sturgeon spawning location is affected by the elevation of Kootenay Lake (Duke, et al. 1999, Paragamian et al. 2002).  Since operation of Libby Dam began, Kootenay Lake is now held more than 2 m lower in spring than pre-dam elevations.  Contract studies with the U. S. Geological Survey are ongoing to determine the interaction of flow/velocity/and lake elevation in the white sturgeon spawning location as well as sediment transport and deposition studies.  More recent analysis of USGS data suggests white sturgeon are selecting zones in the spawning reach of accelerating velocity for spawning sites.  This analysis is expected to continue into 2005 to help determine why white sturgeon select the spawning sites they do and resolve why they do not move further upstream to more suitable habitat.


Increased concern for the spawning location (over sand substrate) of Kootenai River white sturgeon and the fate of eggs and larvae has prompted two adaptive hypothesis tests to help resolve the issue.  First the experimental release of hatchery propagated white sturgeon larvae over sand or cobble substrate.   This experiment was done in 2000, 2001, 2002, and 2003.  The results from survival of these fish is pending.  But most importantly we were able to recapture larva hatchery sturgeon after their release.  This demonstarted that our gear is adequate to capture wild larval fish if they are present.   A second experiment is to unite white sturgeon spawners with suitable substrates (rkm 262) and determine if relocated sturgeon will spawn, "Set and Jet".  A pilot study in 2003 included capturing and moving mature white sturgeon to suitable spawning habitat, monitoring their movement, and any spawning activity.  Twelve white sturgeon (nine males, three females) were moved upstream to the Hemlock Bar reach in 2003 as part of the "Set and Jet" program.  Radio and sonic transmitters were attached to four males and three females.  The first white sturgeon were moved upstream on April 3rd, 2003 and the last on June 19th, 2003.    Movement patterns varied among individuals, but two females and two males stayed in the area for at least one week, and one female and two males moved out of the area immediately.  Five white sturgeon eggs were collected June 5th, 2003 below Hemlock Bar (rkm 261.8).  All eggs collected were too early in development to determine if fertilization had occurred.  Depth and current velocity variables were collected from rkm 261.0 to 262.0 at 100-meter intervals.  Within this reach, depth ranged from 1 to 13 meters (avg 5.7 m), and current velocity ranged from 0.02 to 1.9 m/sec (avg 0.59 m/sec).  Depth and current velocity at the egg collection site was 7 m and 0.52 m/sec, respectively.  Temperature during the time of egg collection was 10.6o C, and discharge at Bonners Ferry was 575 m3/s.  Habitat use was determined subjectively, and most individuals in the study reach seemed to prefer deeper pools with relatively low current velocities.  Many of the individuals were found along rock ledges.  Larval sampling failed to document any recruitment from any successful spawning in the Hemlock Bar reach.  The set and jet program was repeated in 2004 with increased sampling intensity, a defined early relocation group and late relocation goup of sturgeon, and increased monitoring and evaluation effort.  However, in 2004 no eggs were found and females movced out of the reach and back downstream while late release males tended to remain longer than the early release fish.  A third investigation in 2005 will experiment with the release of embryos and their release in the canyon reach.  

This Workplan proposal also addresses the need to evaluate winter flows to allow migration passage of burbot to traditional spawning locations in Idaho, the enhancement of the redband rainbow trout fishery, and the recovery of bull trout.  The following narratives explain study designs to determine recovery strategies.

The burbot in the Kootenai River may be near demographic extinction and a recent population estimate indicates there may be fewer than 600 fish present in Idaho and British Columbia (Paragamian and Whitman 2000).  Mitochondrial DNA (MtDNA) analysis of burbot in the Kootenai River indicated fish in Idaho and British Columbia are of similar genetic makeup but differ significantly from burbot in the Kootenai River, Montana (Paragamian et al. 1999). Behavior studies (Colin Spence, British Columbia Ministry of Water, Land and Air Protection, personal communication) and genetic analysis of mtDNA of burbot from Duncan Lake, British Columbia, indicates these fish are suitable for use as a donor stock to refound spawning in Idaho tributaries as a potential recovery strategy. Test flows to study burbot migrations during the winter of 1997-1998 indicated significantly (p=0.01) more movement of fish during the low flow conditions but movement upstream was significantly (p=0.01) more frequent in January (Paragamian 2000). These findings were supported by findings during the winter of 2000-2001 when the Kootenai River was at 65% of normal flow (Kozfkay and Paragamian 2002).  For the first time since the study began, gravid burbot were captured in Idaho pre-spawn and several were recaptured post-spawn showing evidence of having spawned.   Analysis of a six year data base of burbot telemetry indicated flows of about 200 m3/s from Libby Dam for a period of 90 d or more would be ideal for burbot spawning migration (Paragamian et al. 2005).  

Prior to the winter of 2000-2001 many burbot in the Kootenai River showed evidence of failing to spawn, but it is not known if this is due to warmer winter temperatures,  disruption in spawning synchrony or stress (Paragamian 2000).   Analysis of plasma steroids in the blood of burbot captured during the winter of 2000-2001 showed no evidence of stress (Kozfkay and Paragamian 2002).  Blood samples were also taken during the winter of 2001-2002 but we were not only concerned because the sample size was too low for an evaluation but it was discovered there may be a mortality risk when blood is drawn.  Thus further investigations would benefit from laboratory stress and temperature tests of burbot rather than field studies.  Unfortunately burbot were unavailable for study and studies outside of the basin are unlikely.    

A multi-agency international Burbot Conservation Committee was formed in 1998 and a Conservation Strategy was produced.   On February 2, 2000 conservation groups petitioned the USFWS to list burbot under ESA.  After a lawsuit threat the USFWS released a 90 day finding and after a second threat the USFWS made a decsion in 2002 not to list Kootenai River burbot.  A Kootenai Valley Resource Initiative (KVRI) was organized during the winter of 2001-2002 and a Burbot Subcommittee was formed to shepard the Conservation Strategy and move it into a Conservation Agreement.   The KVRI is comprised of local government and managing agencies on the Kootenai River.  A final draft of a Kootenai River burbot Conservation Strategy and Memorandum of Understanding (MOU) was completed in February 2005.   The MOU is now ready for signiture of managing agencies.

Declines in other fish populations such as kokanee, bull trout, and redband rainbow trout populations in the Kootenai River have also been documented.  Bull trout are native to the Kootenai River in Idaho and the species was declared threatened in 1998 by the USFWS under the ESA.  Although we have little knowledge regarding bull trout populations and life history in the Kootenai River recent surveys of North and South Forks of Callahan Creek, in Idaho, during 2002-2003 indicates this is an important spawning location.  It is not known if these are resident bull trout, fluvial or adfluvial.  Continued research conducted on bull trout will be valuable in directing management strategies aimed at conservation and recovery of the species in Idaho.  Redband rainbow trout are also native to the Idaho reach of the Kootenai River and were unsuccessfully petitioned in 1994 for protection under the ESA.  Research conducted into the life history, distribution, and abundance of redband rainbow trout will enhance our ability to manage the species effectively and reduce the risk of future listing under the ESA.

Other research has concentrated on bull trout life history for the Idaho part of the drainage. According to radio-tagging studies, O'Brien Creek, Montana is an important spawning tributary. We have also observed bull trout spawning in Boulder and N. and S. Callahan creeks, the first documented in the Idaho portion of the Kootenai drainage. Whether these spawners are from a resident fluvial, fluvial or adfluvial population is unknown. The Callahan drainage is also rearing habitat for bull trout from age-0 through at least age-2.

Recent trout research from 2001-2003 concentrated on determining recruitment sources to the Kootenai River upstream of Bonners Ferry. We have tracked radio-tagged rainbow trout to determine spawning tributaries, and measured juvenile rainbow trout out-migration from tributaries. Our data suggest that Boulder Creek is the largest source of recruits to the Kootenai River in Idaho, and Callahan Creek is an additional source. Two smaller streams, Caboose and Debt creeks, also contribute age-0 rainbow trout recruits. However, these streams have perched culverts that are potential upstream migration barriers to adult rainbow trout. These streams also have aggraded alluvial fans at their mouths that often block juveniles from out-migrating in the summer.

Applications of the trout research have included implementation of a size and bag limit on trout in the Kootenai River due to high fishing mortality; identifying bull trout redd count index transects on N. and S. Callahan creeks for continued ESA monitoring; and flow measurements at several culverts to determine if they are fish passage barriers.  In 2005 a creel survey will be implemented to help determine the affect of recent restrictive angling regulations on the rainbow trout fishery.  The new regulations include a two fish creel limit and a minimum length limit of 16 inches (406 mm).  The regulation change was made to give all rainbow trout the opportunity to spawn at least twice before they were of legal length for harvest.

Further research could concentrate on increasing recruitment from Boulder Creek, such as with nutrient supplementation. Finally, the Deep Creek drainage is important adfluvial rainbow trout spawning and rearing habitat, but is highly impacted by man. Determination of potential habitat conservation and restoration in this drainage would likely benefit the rainbow trout population.  In addition monitoring and evaluation studies could demonstrate the benefits of ongoing nutrient addtions, to the South Sarm of Kootenay Lake, to adfluvial rainbow trout that spawn in the Deep Creek drainage.


Mountain whitefish are the most frequently caught sportfish in the Kootenai River, Idaho (Paragamian 1995).  Based on population estimates at the Hemlock Bar reach of the river, the mountain whitefish population has decreased since shortly after operation of Libby Dam began (Partridge 1983; Downs 2000; Walters and Downs 2001; Paragamian 2002). A likely factor contributing to this trend is the reduced secondary productivity of the Kootenai River. Nutrients are nearly depleted by the time the river reaches Idaho (Woods 1982; Snyder and Minshall 1996). Hauer and Stanford (1997) found a change in Kootenai River benthos species composition with reduced numbers of Plecoptera and Tricoptera pre and post-Libby Dam.  Factors with the potential to limit recovery of fish populations, including discharge patterns from Libby Dam as well as primary and secondary productivity, should be evaluated for possible enhancement.

Large scale fish electrofish sampling on the Kootenai River will continue into 2005.  However, the sample sites in the upper sections of the river showed to be dominated by mountain whitefish, while the lower sites showed more  northern pikeminnow, largescale sucker, peamouth chub, and redside shinners.  In terms of total fish caught per unit of effort, the samples ranged from 217 fish/h at rkm 251 (Cow Crk) to 330 fish/h at rkm 230 (Shorties Is).  In terms of total fish biomass per unit of effort, the samples ranged from 21.3 kg/h at rkm 230 to 81.8 kg/h  at rkm 265 (Hemlock Bar).

A cooperative study with the KTOI has explored the prospects of restoring nutrients to the Kootenai River [Adaptive Environmental Assessment (AEA)] which may benefit all native fish populations (Paragamian 2002).   The first phase of AEA was held during the summer of 1997 and was completed in 1998. A users manual was prepared to enable individual researchers from the cooperative agencies to use the Kootenai River AEA model (Josh Korman, University of British Columbia, unpublished document).  The second phase of the AEA process examined available information to determine data gaps for further planning and implementation of the concept of adding nutrients to the river. This second phase was initiated in 1999 and is expected to be completed through efforts of IDFG and KTOI and a AEA workshop held in 2004 with the new information collected.  This second phase is referred to as "large scale sampling" and includes studies of pre-treatment water quality, primary production, macroinvertebrates, fish community structure, and creel surveys. These findings have been used to build a database to determine benefits of nutrient restoration to the restoration of native fish and angler harvest.  Nutrient restoration is a viable and  nutrient restoration experiments are proposed for 2005 to improve trophic prduction at all levels.

With all of the information logged in, a cost analysis was performed on how much fertilizer would be needed to elicit a desired result in nutrient levels of the upper river.   In November, 2003, metals analysis was performed on 14 mountain whitefish and largescale suckers in the proposed fertilization reach.  These metals, although above detection limits, are considerably lower than USEPA and International limits for human consumption.  In winter of 2004-2005 permits through the EPA, Idaho DEQ, USFWS, USACE, and USFS were being processed to comply with all NEPA and environmental standards.