Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
SOW Report
Contract 65704: 1995-004-00 EXP LIBBY RESERVOIR MITIGATION PLAN
Project Number:
Title:
Libby Reservoir Mitigation Restoration and Research, Monitoring and Evaluation (RM&E)
BPA PM:
Stage:
Implementation
Area:
Province Subbasin %
Mountain Columbia Kootenai 100.00%
Contract Number:
65704
Contract Title:
1995-004-00 EXP LIBBY RESERVOIR MITIGATION PLAN
Contract Continuation:
Previous: Next:
58082: 1995-004-00 EXP LIBBY RESERVOIR MITIGATION PLAN
  • 69668: 1995-004-00 EXP LIBBY RESERVOIR MITIGATION PLAN
Contract Status:
Closed
Contract Description:
Note to Contract Officer:  Send contract documents to Mike Burke, mburke@mt.gov.

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 plans to continue our ongoing long-term multi-year revegetation efforts on two of our previously completed restoration projects (Grave and Therriault Creek Projects) during the next year (WEs I, Jand K, respectively).  We also propose to complete as needed maintenance to several of our other previously completed stream restoration/mitigation projects (WE L).  

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 and Stephens 2011).  Previous investigators (Marshall 2007; Sylvester and Stephens 2011) found that infestations of D. geminata are most severe immediately downstream of Libby Dam, which contributes to timing and distribution of this nuisance algae.  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 which will contribute to the understanding of D. geminata blooms in the Kootenai River below Libby Dam, 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 a rigorous monitoring and evaluation program to investigate the efficacy of our restoration efforts (WEs C and G).  This work also includes maintaining previously completed projects (WE L).    

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.  Montana FWP (2012) estimated that angling pressure equaled 18,447 angler days for the entire year of 2011, and 12,960 for the period May through September.  The tailrace fishery is an especially popular trophy rainbow trout fishery, which produced the current Montana State record rainbow trout (33.1 pounds) in 1997.  Little is known about the relative importance of source tributary populations to Kootenai River recruitment or the factors that influence growth and survival of Kootenai River fishes.  In 2011, MFWP initiated a multi-year applied research effort to address these uncertainties.  

Important spawning and recruitment tributaries/sources 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 was 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 attempted to develop methodologies during our previous contract period to assign fish of unknown origin captured within the Kootenai River to their population of origin using genetic methodologies (Leary 2013).  However, the attempt was not successful due primarily to high hybridization levels and individuals from more than one randomly mating population present in several of the potential source tributaries (Leary 2013).  MFWP proposes to continue this research effort using an alternate methodology (stable isotope signatures) 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).  

MFWP initiated a multi-year applied research study in 2011 to investigate the growth and survival of Kootenai River fishes in order to not only quantify these two important population dynamic attributes, but to also determine important physical and biological conditions that influence these two processes.  The ultimate objective is to identify important covariates 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 proposed work is expected to continue for two additional years, and includes work identified under WEs (E and G), within this contract period.  This study is a collaborative effort between Project 199500400, 200600800, and the MFWP Fisheries Management Program.  

Objective 4:  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 (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 (N, P and Q).
Account Type(s):
Expense
Contract Start Date:
07/01/2014
Contract End Date:
06/30/2015
Current Contract Value:
$801,001
Expenditures:
$801,001

* Expenditures data includes accruals and are based on data through 30-Nov-2021.

BPA CO:
BPA COTR:
Env. Compliance Lead:
Work Order Task(s):
Contract Type:
Contract (IGC)
Pricing Method:
Cost Reimbursement (CNF)
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Full Name Organization Write Permission Contact Role Email Work Phone
Matt Boyer Montana Fish, Wildlife and Parks (MFWP) Yes Contract Manager mboyer@mt.gov (406) 751-4570
Cecilia Brown Bonneville Power Administration Yes COTR ckbrown@bpa.gov (503) 230-3462
Mike Burke Montana Fish, Wildlife and Parks (MFWP) No Administrative Contact miburke@mt.gov (406) 444-3301
James Dunnigan Montana Fish, Wildlife and Parks (MFWP) Yes Technical Contact jdunnigan@mt.gov (406) 293-4161x200
Brian Marotz Montana Fish, Wildlife and Parks (MFWP) No Supervisor bmarotz@mt.gov (406) 751-4546
Solomonn Marsh Bonneville Power Administration No Contracting Officer spmarsh@bpa.gov (503) 230-3943
Jennifer Snyder Bonneville Power Administration Yes Env. Compliance Lead jasnyder@bpa.gov (503) 230-4187
Amber Steed Montana Fish, Wildlife and Parks (MFWP) Yes Technical Contact asteed@mt.gov (406) 751-4541
Ryan Sylvester Montana Fish, Wildlife and Parks (MFWP) Yes Technical Contact rsylvester@mt.gov (406) 293-4161x203
Dorothy Welch Bonneville Power Administration Yes F&W Approver dwwelch@bpa.gov (503) 230-5479


Viewing of Work Statement Elements

Deliverable Title WSE Sort Letter, Number, Title Start End Complete
Environmental documentation for all activities requiring such review A: 165. EC work as appropriate for the different work elements 06/30/2015 06/26/2015
Mitigation projects identified, prioritized, and selected B: 114. Identify and Select Projects 06/30/2015 06/26/2015
Libby Dam Mitigation project monitoring and evaluation completed and summarized in annual report C: 157. Monitor and Evaluate Mitigation Projects for Effectiveness. 04/30/2015 04/30/2015
Monitor trend/status of Montana focal species. D: 157. Monitor trend and status of focal species in MT portion of Kootenai Basin 06/30/2015 06/26/2015
Estimates of growth and survival for Kootenai River trout. E: 157. Estimate growth and survival of trout in the Kootenai River 03/31/2015 03/24/2015
Kootenai River Project Fish population Control Site information F: 157. Conduct Fish Sampling in the Kootenai River (Yaak Section): Data Collection 01/30/2015 01/30/2015
Analyze and interpret Libby Mitigation physical and biologic data. G: 162. Analyze and interpret Libby Mitigation physical and biologic data 03/31/2015 03/31/2015
PIT tagged Kootenai River resident trout and burbot H: 158. Mark rainbow trout and burbot in Kootenai River below Libby Dam 03/31/2015 03/31/2015
Riparian vegetation maintenance for the Therriault Creek Restoration Project. I: 198. Maintain riparian vegetation on Therriault Creek Project. 11/28/2014 11/28/2014
Therraiult Creek Revegetation Maintenance and Monitoring Report. J: 141. Produce effectiveness monitoring report for Therrriault Creek Project 02/27/2015 12/31/2014
Grave Creek Riparian Vegetation Restoration Project Maintenance K: 198. Maintain riparian vegetation on Grave Creek Project 11/28/2014 11/28/2014
Exiting restoration projects repaired and maintained. L: 186. Conduct Maintenance on Previously Completed Mitigation Projects 06/19/2015 06/19/2015
Didymosphenia geminata research project M: 157. Didymosphenia geminata research 06/30/2015 06/26/2015
Watershed restoration plan for the Fisher River. N: 174. Develop a watershed restoration plan for the Fisher River 06/30/2015 06/26/2015
All administrative tasks fulfilled with timely quality products O: 119. Manage and Administer Projects for the Libby Mitigation Program. 05/29/2015 05/29/2015
Attach Progress Report in Pisces Q: 132. Progress Report for the period July 1, 2012 to Dec 31, 2014 03/15/2015 03/12/2015

Viewing of Implementation Metrics
Viewing of Environmental Metrics Customize

Primary Focal Species Work Statement Elements
Burbot (Lota lota)
  • 1 instance of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 158 Mark/Tag Animals
Cutthroat Trout, Westslope (O. c. lewisi)
  • 2 instances of WE 198 Maintain Vegetation
  • 1 instance of WE 186 Operate and Maintain Habitat/Passage/Structure
  • 1 instance of WE 114 Identify and Select Projects
  • 1 instance of WE 174 Produce Plan
  • 5 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 158 Mark/Tag Animals
  • 1 instance of WE 162 Analyze/Interpret Data
Trout, Bull (S. confluentus) (Threatened)
  • 2 instances of WE 198 Maintain Vegetation
  • 1 instance of WE 186 Operate and Maintain Habitat/Passage/Structure
  • 1 instance of WE 114 Identify and Select Projects
  • 1 instance of WE 174 Produce Plan
  • 4 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 158 Mark/Tag Animals
  • 1 instance of WE 162 Analyze/Interpret Data
Trout, Rainbow (Oncorhynchus mykiss)
  • 3 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 158 Mark/Tag Animals
  • 1 instance of WE 162 Analyze/Interpret Data
Trout, Interior Redband (O. mykiss gairdnerii)
  • 1 instance of WE 186 Operate and Maintain Habitat/Passage/Structure
  • 1 instance of WE 114 Identify and Select Projects
  • 1 instance of WE 174 Produce Plan
  • 5 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 158 Mark/Tag Animals
  • 1 instance of WE 162 Analyze/Interpret Data
Whitefish, Mountain (Prosopium williamsoni)
  • 2 instances of WE 157 Collect/Generate/Validate Field and Lab Data

Sort WE ID WE Title NEPA NOAA USFWS NHPA Has Provisions Inadvertent Discovery Completed
A 165 EC work as appropriate for the different work elements 07/01/2014
B 114 Identify and Select Projects 07/01/2014
C 157 Monitor and Evaluate Mitigation Projects for Effectiveness. 07/01/2014
D 157 Monitor trend and status of focal species in MT portion of Kootenai Basin 07/01/2014
E 157 Estimate growth and survival of trout in the Kootenai River 07/01/2014
F 157 Conduct Fish Sampling in the Kootenai River (Yaak Section): Data Collection 07/01/2014
G 162 Analyze and interpret Libby Mitigation physical and biologic data 07/01/2014
H 158 Mark rainbow trout and burbot in Kootenai River below Libby Dam 07/01/2014
I 198 Maintain riparian vegetation on Therriault Creek Project. 07/01/2014
J 141 Produce effectiveness monitoring report for Therrriault Creek Project 07/01/2014
K 198 Maintain riparian vegetation on Grave Creek Project 07/01/2014
L 186 Conduct Maintenance on Previously Completed Mitigation Projects
M 157 Didymosphenia geminata research 07/01/2014
N 174 Develop a watershed restoration plan for the Fisher River 07/31/2014
O 119 Manage and Administer Projects for the Libby Mitigation Program. 07/01/2014
P 185 Periodic Status Reports for BPA 07/01/2014
Q 132 Progress Report for the period July 1, 2012 to Dec 31, 2014 07/01/2014