Note to Contract Officer:  Send contract documents to Karen Zackheim, administrative contact.

PROJECT BACKGROUND

Fisheries losses caused by the construction and operation of Libby Dam, site-specific mitigation actions and monitoring strategies were documented in the Libby Dam Fisheries Mitigation and Implementation Plan (MFWP et al. 1998).  As directed by the Northwest Power and Conservation Council's (NPCC) Fish and Wildlife Program (NPCC 1994 and 2000), the  Mitigation Plan and Kootenai Subbasin documents present actions needed to offset fisheries losses associated with the construction and operation of Libby Dam. These documents were developed collaboratively with the Confederated Salish and Kootenai Tribes (CSKT) and the Kootenai Tribe of Idaho (KTOI).  Mitigation actions are also coordinated with the Idaho Department of Fish and Game (IDFG) and British Columbia Ministries.

This program implements the NPCC Plan to enhance hydropower-affected fish stocks in the Montana portion of the Kootenai Watershed.  Fish restoration efforts in this work plan are consistent with the White Sturgeon Recovery Plan (USFWS 1999) and the 2006 White Sturgeon Biological Opinion (BiOp) on the operation of the Federal Columbia River Power System (FCRPS).  Kootenai River white sturgeon (Accipenser transmontanus) are endangered; less than 600 individuals remain. Bull trout (Salvelinus confluentus) are listed as threatened under ESA, and populations in the Kootenai River were fragmented by Libby Dam. The abundance and distribution of westslope cutthroat trout (Oncorhyncus clarki lewisi) and redband trout (O. mykiss) in the Kootenai Basin have  declined from their historic condition due to dam construction and operation, negative interactions with nonnative species (e.g. predation, competition, genetic introgression), and anthropogenic factors (e.g. channel alterations and sedimentation). Hybridization and competition with non-native fish species and habitat degradation pose the greatest threat to westslope cutthroat trout.   This work plan implements and evaluates on-the-ground habitat enhancement efforts that alleviate limiting factors to native species populations. Projects reclaiming critical spawning, rearing, and over-wintering habitats have been completed, or are ongoing.  These projects are being completed with the help of grassroots watershed work groups comprised of landowners, agencies, sportsmen's groups and local, state and federal government coalitions.

Project history  

This project combines the former projects 83-465-00, 83-467-00 and 94-010-00 for efficiency and cost savings.  Work on Libby Reservoir to assess the effects of operation on fish populations and lower trophic levels began in 1982.  This project established relationship between reservoir operation and biological productivity, and incorporated the results in the computer model LRMOD.  The models and preliminary IRCs (Integrated Rule Curves, originally called Biological Rule Curves) were first published in 1989 (Fraley et al. 1989), and then refined in 1996 (Marotz et al. 1996 and 1999).  The IRCs were adopted by NPPC in 1994, but were superseded by operations called for by the NMFS 1995 Biological Opinion and have not yet been implemented.  

This Project established a long-term database to monitor population trends for kokanee, bull trout, westslope cutthroat trout, rainbow trout, burbot and other native fish species.  Long-term monitoring programs of zooplankton and trophic relationships were similarly established.  A model was calibrated to estimate the entrainment of fish and zooplankton through Libby Dam as related to hydro-operations and use of the selective withdrawal structure. Research on the entrainment of fish through the Libby Dam penstocks began in 1990, and results were published in 1996 (Skaar et al. 1996). Assessment of the effects of river fluctuations on Kootenai River burbot fishery was examined in 1994 and 1995. The effects of dam operation on benthic macroinvertebrates in the Kootenai River was also assessed (Hauer and Stanford 1997) for comparison with conditions measured in the past (Perry and Huston 1983).  This study was replicated in 2005 with the addition of examining the effect of a nuisance diatom (Didymosphenia geminate) on the benthic community (Marshall 2007).  The Libby Project has also identified important spawning and rearing tributaries and conducted genetic inventories in the Montana portion of the Kootenai Watershed for bull, westslope cutthroat, and redband trout.  This project developed a non-lethal genetic methodologies to differentiate between native redband trout and non-native rainbow trout (Brunelli et al. 2008), and a non-lethal genetic methodology to identify natal tributary origin for bull trout in the upper Kootenai Watershed and quantify bull trout entrainment at Libby Dam (Ardren et al. 2007).   Research on the effects of operations on the river fishery using IFIM techniques was initiated in 1992. The results of this study were recently finalized and upgraded with the incorporation of GIS technology (Miller and Geise 2004). The final result was a model capable of graphically and numerically quantifying weighted usable area for juvenile and adult rainbow trout and bull trout in the Kootenai River for a wide range of discharges.  

Scientific Framework

We have designed our program to address fisheries issues in varying levels of scope, descending from basin-wide, over-arching mitigation requirements to site-specific actions.  Mitigation projects are selected and prioritized primarily on the Kootenai Subbasin Plan.  We have further outlined our rationale and decision pathway within this document (see below).  The scientific framework addresses varying levels of scope, progressing from basin-wide issues toward site-specific details. Each level is addressed by individual mitigation actions. Our first priority is to prevent impacts that can reduce the overall health of the subbasin.  Basin-wide issues include federal and private dam operations and the prevention or containment of invasive aquatic nuisance species. Onsite mitigation addresses habitat degradation, fish passage barriers, genetic introgression with pure native fish stocks and negative interactions between native and nonnative fish species. Offsite mitigation presents opportunities to create genetic reserves to conserve native species and to increase angling opportunities.

Modifications to dam operation are a basin-wide mitigation requirement because of the far-reaching influence of dam operation on environmental conditions in the reservoirs and rivers throughout the Columbia River Basin. Montana has actively pursued a basin-wide operating strategy beneficial to imperiled fish stocks in the Columbia River headwaters, as well as the lower river. In the Libby Mitigation Plan, we estimated that approximately half of the losses identified within the loss statement (MFWP, CSKT and KTOI 1998) could be mitigated by modifying dam operation.  Much of the remaining losses can be mitigated using techniques that do not require changes in reservoir or river management.  

The overall goal of the Libby Mitigation Project is to correct effects caused by the Federal hydropower operations and mitigate for fisheries losses attributed to the construction and operation of Libby Dam using watershed-based, habitat enhancement, fish passage improvements, and offsite fisheries habitat improvement measures. The Libby Mitigation Project's Work Elements (WE) for the current funding cycle have been organized around the following five objectives.  

Objective 1:  Restore, enhance, or protect and maintain existing sustainable native fish populations and their habitat in the Kootenai Basin in order to mitigate for losses attributable to the construction and operation of Libby Dam.

The Libby Mitigation Project has a solid track record of achieving effective mitigation projects within the Montana portion of the Kootenai Subbasin (Dunnigan et al. 2003; 2004; 2005; 2007).  We continue to improve existing habitat conditions within the basin through our proactive restoration program.  Our program specifically identified three high priority projects scheduled for implementation during the 2009 FY.  Work is scheduled to continue our restoration activities on Young, Therriualt, Grave, and Libby creeks (WEs A, B, E, F, and J respectively).  During the FY09 period we will complete the second phase of restoration of Loon Lake.  This project will remove non-native species from this system, replacing them with westslope cutthroat trout.  This work is identified under WE D.    

Objective 2:  Monitor and evaluate the efficacy of previously completed restoration/mitigation projects.    

The Libby Mitigation Project is committed to monitoring and rigorously evaluating our restoration efforts.  This work also includes maintaining previously completed projects.  This work is identified under WEs H and I.  
        
Objective 3:  Collect, analyze and interpret spatial distribution, seasonal movement, population trend, and growth data, absolute and relative abundance  indices, and genetic and life history information needed for the conservation and recovery of native resident fish species including the endangered Kootenai River white sturgeon, threatened bull trout, westslope cutthroat trout, interior redband rainbow trout, and burbot, as outlined in the Libby Mitigation and Implementation Plan (MFWP et al. 1998) and Kootenai Subbasin Plan.

Montana FWP has developed several monitoring strategies specifically designed to investigate the life history and limiting factors of bull trout within the Kootenai Subbasin.  We have documented that hydro operations at Libby Dam are responsible for substantial bull trout entrainment.  WEs K, N, Q, and T are intended to further monitor the levels of impact of hydro operations on the bull trout populations in the upper Kootenai system.  Work Elements are also included within this SOW that are intended to quantify bull trout abundance through redd counts (WE M), adult population estimates (WE N), and habitat related factors (WE L).  These efforts will be analyzed under WE T.  

Montana FWP has collected zooplankton from Libby Reservoir since 1983 in an attempt to relate changes in density and structure of the community to parameters of other aquatic communities, as well as to collect data indicative of reservoir processes, including aging and the effects of reservoir operation.  This work will continue under WE R.  

Montana FWP has used gillnets since 1975 to assess annual trends in fish populations and species composition in Koocanusa Reservoir.  These yearly sampling series were accomplished using criteria established by Huston et al. (1984).  Seasonal gillnetting on Koocanusa Reservoir and conducts this monitoring annually from April through November, and is identified under WE Q.  

Objective 4:  Investigate the factors limiting the production and recruitment of salmonid populations in the lower Kootenai River (Kootenai Falls to Idaho border). This is a collaborative project between the KTOI, IDFG and MFWP.  The Montana section of the Kootenai River will serve as a control for Idaho's fertilization project.  All collaborators identified this section of the river to best serve this purpose.   This work is identified under WE P.  

Objective 5:  Summarize, evaluate, analyze, discuss and disseminate information gathered during project activities in a scientific format.  This work will be accomplished primarily through public meetings, project annual reports, and status reports and is identified under WEs V and W.