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 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 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; 2009; 2010; 2011).  We continue to improve existing habitat conditions within the basin through our proactive restoration program.  Our program identified several high priority projects scheduled for implementation during the next two years.  Montana FWP proposes to continue our multi-year phased approach of revegetating the Grave and Therriault creek restoration projects (WEs I, and L, respectively).  We propose to eradicate an illegally introduced population of northern pike in Bass Lake (WE N), which has been identified as the likely source of northern pike recently observed in Koocanusa Reservoir.  During FY2014, non-native rainbow trout will be removed from Howard Lake in order to minimize hybridization with native redband trout in the upper Libby Creek watershed (WE P).  We propose to develop a revegetation plan a portion of Young Creek, an important westslope cutthroat trout tributary to Koocanusa Reservoir in FY2013 and implement that plan in FY14 (WEs O and R, respectively).  During FY14, we also propose to continue the second phase of fish screening on Deep Creek, a tributary to the Tobacco River, and an important rearing and spawning tributary for cutthroat and bull trout (WE Q).  We also propose to develop a conceptual restoration plan for lower Dunn Creek, and important spawning tributary for large rainbow trout inhabiting the Kootenai River below Libby Dam (WE T).  

The Libby Mitigation Project is also initiating a three year research project to investigate factors that affect the distribution and abundance of D.  geminata in the Kootenai River below Libby Dam.  D. geminata became established in the Kootenai River below Libby Dam in the early 2000's where it frequently forms dense mats on the river bottom that interfere with recreational opportunities for fishers, but more importantly may be negatively affecting the trophy rainbow trout fishery because of reduced abundance of desirable large invertebrate prey (Marshall 2007; Sylvester 2011).  Prolific growths of periphyton in natural waters are typically indicative of elevated nutrient concentrations and associated with eutrophication, which is the input of excess nutrients; commonly phosphorus (P) in freshwaters (Schindler 1974).  D. geminata is somewhat of an enigma compared to most fresh water algae, in that D. geminata often forms nuisance blooms in oligotrophic (dissolved P < 2.3 µg/L) conditions (Kilroy and Bothwell 2012; Bothwell and Kilroy 2011; but see Kawecka and Sanecki 2003 for occurrence of blooms in high P conditions).  Libby Dam clearly traps nutrients within the reservoir and reduces the productivity of the Kootenai River downstream of Libby Dam (Gidley 2009). The overarching objective of the proposed research is to test a suite of hypotheses aimed to contribute to the understanding of D. geminata blooms in the Kootenai River below Libby Dam in Montana with the potential to indicate practical methods of remediation (reduction in severity or frequency of occurrence) of blooms.  This research effort is identified under WE (M).

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 (WEs C and G).  This work also includes maintaining previously completed projects (WE 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 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 abundance through redd counts, and habitat related factors (WEs D and G).    
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 during this contract period under WEs (D and G). 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), including seasonal gillnetting on Koocanusa Reservoir conducted annually from April through November.  This work will continue during this contract period (WEs D and G).

The Montana portion of the Kootenai River is very popular recreational fishery in the Montana portion of the subbasin, second in annual angler trips only to Koocanusa Reservoir.  McFarland and Dyskstra (2010) estimated that angling pressure equaled 30,575 angler days for the entire year of 2009, and 21,645 for the period May through September.  The tailrace fishery is an especially popular trophy rainbow trout fishery.  Montana FWP manages the Libby Dam tailrace section of the Kootenai River for trophy rainbow trout.  The current Montana State record rainbow trout (33.1 pounds) was captured below Libby Dam in 1997, and is especially known to produce trophy class rainbow trout.   The current fishing regulations on the Kootenai River from Libby Dam downstream to the Fisher River confluence (3.5 miles) allow angling between June 1 to March 31, harvest of four combined trout including three fish under 13 inches and one fish over 24 inches.  The limit applies to both the daily and possession limits.  The large rainbow trout are known to spawn in the tailrace area, and MFWP has conducted visual redd counts within the tailrace area since 1987 (MFWP, unpublished data).  MFWP has also conducted mark recapture population estimates within the Libby Dam tailrace since 2008, and observed a precipitous decline in rainbow trout abundance within this section, especially for rainbow trout larger than 400 mm, but has not been able to generate reliable estimates of abundance of fish larger than 24 inches (610 mm) (MFWP, unpublished data).   Project 199500400 designed and implemented a creel survey to estimate fishing effort, catch and harvest of trout in the Kootenai River downstream of Libby Dam during the 2009/2010 fishing season which included the period June 1, 2009 to March 31, 2010 (Dunnigan et al. 2011).  This creel survey targeted the rainbow and bull trout fishery, and was conducted during the night and crepuscular hours.  We estimated that 27 rainbow trout >24 inches were harvested in this fishery.  These results in part prompted fisheries managers to implement more restrictive harvest regulations in this section of the river for the 2012 season.  The ultimate source of the large rainbow trout in the Libby Dam tailrace section is not known.  Furthermore, important spawning and recruitment tributaries of the Kootenai River have not been identified.  However, recent investigation into the genetic composition of Kootenai River rainbow trout suggests that the component of the fishery which consists of large individuals within the tailrace area may be genetically distinct from other fish within the river, and that substantial genetic diversity occurs in rainbow trout throughout the Montana portion of the Kootenai River (Leary 2010).  Project 199500400 initiated a research project in 2011 to investigate the genetic structure of rainbow trout within the MT portion of the Kootenai subbasin.  There were two primary objectives of this study. Our first objective is to examine how genetic diversity is distributed both within and among potential rainbow trout recruitment sources to Kootenai River. These potential recruitment sources include tailrace spawning, Koocanusa Reservoir entrainment, and tributaries downstream of Libby Dam.  Secondly we want to assess our ability to use genetic markers to assign fish of unknown origin captured within the Kootenai River to their population of origin.  In the summer of 2011, we collected genetic samples from over twenty tributaries.  These samples currently are awaiting genetic analysis, and pending favorable results (genetic differentiation between tributaries), we propose to continue this research project during the current contract period.  Information obtained from this study could help identify those tributaries which are important recruitment sources of rainbow trout in the Kootenai River and prioritize conservation and restoration efforts in the most critical tributaries.  This work activity is identified within the contract under WE (D).  Montana FWP conducts annual mark recapture populations of rainbow trout in the Kootenai River in three sections including the Libby Dam tailrace section (river mile [RM] 218.2-221.7), the Re-Regulation section (RM 213.2-215.1), and the Flower-Pipe Section (RM 201.1-204.0) (Sylvester and Stephens 2011).  We randomly collect scale samples from rainbow trout in order to estimate length at age using methodologies described in Sylvester and Stephens (2011).  

From 2004-2008, MFWP placed PIT tags in rainbow trout > 300 mm collected from the Libby Dam tailrace section in order to estimate annual growth of individual fish, and we also collected scale samples from all PIT tagged fish during this period (Sylvester and Stephens 2011).  We also collected scale samples from all previously PIT tagged fish which were subsequently recaptured.  We recaptured 26 rainbow trout which had at least one year between original capture and recapture (MFWP unpublished data).  This allowed us to complete a blind study to evaluate how well scale readers were able to identify the correct number of annual identifiable on scales collected at the time of original capture and recapture.  Mean total length of trout in this study was 362 mm (range 307-431), and annual growth averaged only 17 mm.  We were only able to identify an additional annuli that should have been present 30% of the time.  Growth rates were slightly larger (average 24 mm/year) for all PIT tagged fish (including those which readable scales were not collected) (MFWP unpublished data).  The disparity between observed annual growth rates and those predicted from back calculated length at age estimates prompted us in 2011 to initiate a larger PIT tagging study on the Kootenai River.   We tagged an additional 2600 trout in 2011 while conducting the population estimates in the three sections.  Our objectives for this work are to  further validate age estimates, especially for smaller rainbow trout (<300mm), estimate relative minimum survival rates between sections, and assess of how various biological and physical conditions (e.g., thermal regime, invertebrate community, fish diets, fish numbers) are affecting fish in these three sections of the Kootenai River. We plan to continue this study for three additional years, including work identified under WEs (E and H), within this contract period.  This study is a collaborative effort between Project 199500400, 200600800, and the MFWP Fisheries Management Program.  

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.  These work activities are identified under WEs (F and G).  

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 (G, U and W).