NOTE TO CONTRACT OFFICER:  Please send contract documents to Mike Burke, Administrative Contact and Matt Boyer, Contract Manager.

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 Plan document 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), the Kootenai Tribe of Idaho (KTOI), and Montana Fish Wildlife and Parks.  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, with approximately 1,000 wild individuals remaining (Beamesderfer et al. 2009). Bull trout (Salvelinus confluentus) are listed as threatened under ESA, and populations in the Kootenai River were fragmented by Libby Dam.  This project implements bull trout restoration efforts that are consistent with the Bull Trout Recovery Plan (USFWS 2002), including restoration and protection of stream segments within streams identified as critical habitat (USFWS 2010) to ensure connectivity to and enhancement of core bull trout spawning and natal tributaries within the Kootenai Subbasin.  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 and redband 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 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.  Although the IRCs were not ever fully implemented, many of the concepts were adopted in the NPCC’s 2004 operating strategy known as the Mainstem Amendments, which were first fully implemented in October 2008.  Project 200600800 assesses the biological and physical effects of Mainstem Amendments at Libby and Hungry Horse Dams.  Project 199500400 works closely with Project 200600800, and collaborates on many efforts within the Kootenai Basin for cost savings efficiency.

The Libby Mitigation 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 et al. 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 geminata (D. geminata) 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 methodology 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; DeHaan et al. 2008; DeHaan and Adams 2011).   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 Columbia 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 for the current funding cycle have been organized around the following objectives.  

Objective 1:  Evaluate impacts of Libby Dam operations on resident fish populations and the food web that supports these fish and their habitats.

Mitigation measures that reduce the impacts of the continued operation of Libby Dam are most effective when reservoir and river management can be modified to offset onsite impacts.  Montana has embraced this strategy and played an important role in developing operational recommendations at Libby Dam.  This overall strategy was also the basis of the development of the Libby Mitigation Plan (MFWP, CSKT, and KTOI 1998) and the Kootenai Subbasin Plan (KTOI and MFWP 2004).  However, operations at Libby Dam have changed substantially since these documents were developed (Sylvester et al. 2016).  
MFWP initiated a multi-year applied research study in 2011 to investigate the growth and survival of Kootenai River fishes to not only quantify these two important population dynamic parameters, but to also determine important physical and biological conditions that influence these two processes.  The ultimate objective is to identify important covariates (including operational factors) that may be used to improve the growth or survival of Kootenai River fishes.  The multi-year field study focuses on four sections of the Montana portion of the Kootenai River where Montana FWP has previously conducted annual mark recapture populations of rainbow trout including the Libby Dam tailrace section (river mile [RM] 218.2-221.7), the Re-Regulation section (RM 213.2-215.1), the Flower-Pipe Section (RM 201.1-204.0), and the Troy Section (RM 183.8-186.2) (Sylvester and Stephens 2011).  The research study will use a mark and recapture study design, and use PIT tags to mark individual fish and estimate annual growth and survival.  The field work for this project was completed during the last contract period, and the results will be analyzed and reported under WEs J and N.  This study has been a collaborative effort between Project 199500400, 200600800, and the MFWP Fisheries Management Program.  Additional efforts to quantify the impacts of changes in operations at Libby Dam are identified in WEs I and J).  

Objective 2:  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. 2003-2017).  We continue to improve existing habitat conditions within the basin through our proactive restoration program.  Our program plans to continue our ongoing long-term multi-year revegetation efforts on the previously completed Therriault Creek restoration project during the next year (WE M).    

Objective 3:  Monitor and evaluate the efficacy of previously completed restoration/mitigation projects.  
  
The Libby Mitigation Project is committed to a rigorous monitoring and evaluation program to investigate the efficacy of our restoration efforts (WEs E and J).    

Objective 4:  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 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 (Ardren et al. 2007; DeHaan and Adams 2011).  Several work elements are intended to further monitor the levels of impact of hydro operations on the bull trout populations in the Kootenai River below Libby Dam.  Work Elements are also included within this SOW that are intended to quantify bull trout relative abundance through redd counts, and habitat related factors (WEs F and J).    

Montana FWP has collected zooplankton from Libby Reservoir since inundation 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 during this contract period under WEs (F and J). Montana FWP has used gillnets since 1975 to assess annual trends in fish populations and species composition in Libby Reservoir.  These yearly sampling series were accomplished using criteria established by Huston et al. (1984), including seasonal gillnetting on Libby Reservoir conducted annually from April through November.  This work will continue during this contract period (WEs F and J).

The Ten Lakes Scenic Area is in northwest Montana, and lies within the Wigwam River watershed. This mountainous region contains several lakes of which the historic fish distribution is largely unknown. However, prior to the development of an MFWP hatchery stock of westslope cutthroat trout in 1970, many of these lakes were stocked with Yellowstone cutthroat trout. Several of these water bodies have been subsequently stocked with hatchery westslope cutthroat trout. The lakes within the Ten Lakes Scenic Area have varying degrees of surface water connection with the Wigwam River and its tributaries. It is currently not known if a Yellowstone cutthroat trout genetic component remains in any of these lakes or if the Yellowstone cutthroat trout genes have influenced the genetic integrity of westslope cutthroat trout populations located downstream of these lakes. This work identified in WEs H and J is intended to investigate this issue. The ultimate goal of this work is to collect the information required to develop a management plan if introgression is indeed an issue.

A similar scenario exists in several mountain lakes within the Cabinet Mountain Wilderness area.  The historic fish distribution of the Cabinet Mountain Lakes is unknown but it is known that these lakes were either fishless or contained either westslope cutthroat trout or redband trout.  However, many of the lakes have been stocked with different fish species including brook trout, westslope cutthroat trout, Yellowstone cutthroat trout or coastal rainbow trout.  Much of the genetic inventory work has been previously completed in most of the fish bearing mountain lakes within the Cabinet Mountains (Huston and Sage 1996), but the critical piece of information that is lacking is the native fish species that occurred within the watersheds that these lakes occur.  This work identified in WEs H and C is intended to investigate this issue. The ultimate goal of this work is to collect the information required to develop a management plan for the Cabinet Mountain Lakes.

Restoration of imperiled fish stocks requires a basic understanding of the life history of those populations, including the habitats used for reproduction and early life stages.  Unfortunately, this basic information is lacking for many important focal species found in Libby Reservoir, including burbot, rainbow and bull trout.  Work identified in WEs K and J identifies a pilot study to test the efficacy of using strontium isotope analysis of resident fish otoliths collected from Libby Reservoir to identify natal tributary of origin.  This will be a two-stage process.  The first stage of this project (2018-2019) will be to collect and analyze water samples and young of the year fish from all major Kootenai River tributaries upstream of Libby Dam (Montana and British Columbia) to determine if spatial differentiation of water chemistry exists within the study area.  The second phase of the effort would be contingent upon favorable results from the first phase.

Objective 5:  Evaluate the efficacy of the Kootenai River Ecosystem Project currently being conducted at the Montana/Idaho border by the Kootenai Tribe of Idaho and Idaho Fish and Game.  

The Kootenai River Ecosystem Project is a collaborative venture between the Kootenai Tribe of Idaho (Project 199404900) and Idaho Fish and Game (Project 198806500) intended to restore the productivity of the Idaho portion of the Kootenai River due to the loss of nutrients locked behind Libby Dam.  Montana FWP contributes to this cooperative project by conducting fish sampling at a control site located upstream of the nutrient addition site.  These work activities are identified under WEs (G and J).  

Objective 6:  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 (A and N).