Project Background

In 2003, the Northwest Power and Conservation Council (Council) directed the Pacific Northwest region to implement and evaluate specific dam operating strategies at Columbia River dams.  Beginning in the summer 2004, reservoir drafts at Hungry Horse and Libby Dams were supposed to be limited to 10 feet from full pool (elevations 3550 and 2449, respectively) during the months of July through September.  During drought years, the reservoir drafts could be increased to 20 feet from full pool by September 30 at each reservoir.  However, the Mainstem Amendments have not been fully implemented to date.  The Mainstem Amendment operations are scheduled to be implemented beginning in water year 2010 (i.e., October 2009).  The Mainstem Amendment dam operation strategy also stabilizes the release of water into the South Fork Flathead and Kootenai Rivers.  These actions were designed to protect aquatic resources in headwater reservoirs and rivers, while providing suitable conditions for anadromous species recovery in the lower Columbia River.  Previous research by Montana Fish, Wildlife & Parks provided empirical data and methods to assess potential impacts of dam operations, including power, flood control and flow augmentation.  Historic river discharge, reservoir elevation, gill netting, and river fish population estimate data provide an environmental base line for comparison with new and alternative operating strategies such as the Mainstem Amendments.  This project will use a combination of research and monitoring to compare the biological and physical responses of fishes and habitat to alternative dam operations upstream and downstream of Hungry Horse and Libby Dams, Montana.  

Project Description

This project will assess the physical and biological effects of a new dam operating strategy at Libby and Hungry Horse Dams, Montana.  The operating strategy known as the Mainstem Amendments was supposed to be implemented in the summer of 2004.  Although it has not officially been implemented to date, current operations by the United States Army Corps of Engineers and Bureau of Reclamation have utilized portions of the Mainstem Amendments, specifically ramping rates.  The Northwest Power and Conservation Council (NPCC) directed the region to test, implement, and evaluate new drafting limits and ramping rates at many of the dams in the Columbia River Basin, known as the Mainstem Amendments.  The new operation strategy limits the summer drafts of Lake Koocanusa, also known as Libby Reservoir, to 10 feet from full pool (surface elevation 2449 feet) during normal water supply years and 20 feet (surface elevation 2439 feet) from full pool during the lowest 20% of water supply years.  The amendments also limit the rates at which discharges into the South Fork Flathead and Kootenai Rivers can be increased or decreased utilizing both daily and hourly limits depending on season and discharge level.  These changes will stabilize flow in the rivers during the productive summer months, while meeting established minimum flows for species such as bull trout.  The new operating strategy may better mediate the needs of all resident fishes throughout the Columbia River Basin with anthropogenic needs including water supply, recreation, and hydropower generation.  This project will use a combination of research and monitoring to quantify and evaluate the effects of the interim operating strategy on the physical and biological communities above and below Libby and Hungry Horse Dams, Montana.

b.  Objectives

Montana Fish, Wildlife & Parks has nine objectives for evaluating the Council's prescribed reservoir operation and discharge ramping rates (i.e., Mainstem Amendments) on fisheries and habitat upstream and downstream of Hungry Horse and Libby Dams, Montana in FY2006.  Some objectives will be completed during FY2006 and others will take several years to complete due to life history aspects of species under investigation and changes in environmental conditions.

Objective 1.   Use LRMOD to calculate the amount of physical habitat available for aquatic productivity resulting from reservoir drafts in the Mainstem Amendments at Libby Reservoir for each water year (i.e., October 1-September 30).  Model simulations will be run using historical and recent Kootenai River and South Fork Flathead River inflow discharges, outflow discharges, and reservoir surface elevation data files collected by the operating or data collection agency (e.g., Bureau of Reclamation, United States Geological Survey, and the United States Army Corps of Engineers).  After each water year is completed, data files will be created and model simulations run.  

Objective 2.   Use LRMOD to calculate the biological responses (e.g., biological production of benthos, invertebrates, zooplankton, primary production) resulting from reservoir drafts in the Mainstem Amendments at Libby Reservoir.  Biological responses will be modeled in a similar fashion to the physical habitat in Objective 1, and utilize the same data files.  

Objective 3.   Compile age, growth, and condition factor data from annual gill net series to compare length at age of kokanee and bull trout under varying reservoir operating strategies.  Relate any variation  in growth or mean length at age to environmental and biological conditions. Spring (i.e., May) and fall (i.e., September) gill net series will be  used as indexes of fish species abundances.  Length and weight data will be used to calculate condition indices for fish species with proposed or accepted standard weight equations.  Gill net data will also be used for collection age estimating structures (e.g., scales and otoliths) for game species and these will be used to estimate ages of fishes and digitize annuli using Optimus software.  Historical gill netting information and scale samples will be used for past growth increment data collection and analysis.  

Objective 4.   Use the Instream Flow Incremental Methodology (IFIM) and RivBio River models to model the amount of physical habitat occurring as a result of historic and recent discharges in the Flathead and Kootenai Rivers as a result of past and recent operating strategies for various life-stages of fishes.  Model simulations will use the same inflow, outflow, and surface elevation files as Objectives 1 and 2.  Model simulations may also be used in coordination with an invertebrate recolonization study of the varial zone to assess the biological productivity lost or impacts to productivity as a result discharge fluctuations.  This objective may also be used in conjunction with 7 to verify existing models of habitat use at various discharge levels in the Kootenai River.  

Objective 5.  Estimate annual salmonid cohort survival, and relate that survival to environmental variables including weekly and daily summer flow variation (tributary and river phase) in the Mainstem Kootenai River.  Cohort survival will be assessed using data from annual population estimates (i.e., age frequency histogram) in the mainstem Kootenai  River collected during the spring and fall population estimates.  Water data (e.g., temperature and discharge data) will be obtained from the United States Army Corps of Engineers.  

Objective  6. Compare length at age, growth increments, and condition of rainbow, westslope cutthroat and bull trout captured downstream of Libby Dam.  Electrofishing surveys for population estimate surveys allows for the collection of age estimating structures and length and weight data.  Subsequent calculation of growth increments and back-calculated length at age and estimation of age can be performed for a variety of fishes.  Fishes that have been injected with PIT tags will also be used for this Objective.  

Objective 7.  Also to evaluate how tributary conditions affect growth, survival, migration patterns, and spawning tributary use of bull trout and other species of fishes in Quartz Creek.  Juvenile population estimates will completed in Quartz Creek using depletion techniques (3-4 downstream passes; reach length 150-200 m) until a 70% depletion efficiency is achieved between consecutive passes.  Age frequencies will be calculated using data and age estimating structures collected during electrofishing surveys or length frequency histograms.  Discharge and water temperature will be collected and the calculated survival and mortality estimates will be related to the biological (e.g., population density, size structure) and physical parameters (e.g., min and max temperature, daily temperature ranges).  PIT tags will also be placed in fishes >125mm to assess growth  under a known set of environmental and biological conditions if recaptured in subsequent years.  A remote PIT tag station (i.e., remote PIT tag reader) was installed in Quartz Creek in August 2007 to assess how tributary conditions (e.g., discharge, temperatures) affect migration patterns of juvenile and adult bull trout and spawning tributary use by adult fishes.   The remote PIT tag station must be maintained on a weekly or biweekly basis to monitor the power supply, remove any debris from the station, and downloading data.  

Objective 8.   A pilot sampling project will begin in the summer of 2009 to assess the catch rates of juvenile and possibly adult white sturgeon from Kootenai Falls to the Idaho border.  Sampling for juvenile and adult white sturgeon has been infrequently performed downstream of Kootenai Falls since the late 1970's and early 1980's.  Stocking of juvenile white sturgeon by the Kootenai Tribe of Idaho occurred  in 1994 and annually since 2004.  Gill nets, angling, and setlines may be used after incidental catch of other species (e.g., bull trout)  is determined.  If mortality of bull trout is high for any gear type, sampling with that gear may be discontinued.   Juvenile sampling will occur from July-September and adult sampling will occur in the spring, May and June.  This objective will not occur if a Section 10 permit is not approved by the United States Fish and Wildlife Service.

Objective 9.  Survey deltas of Kootenai River tributaries to assess the impacts, if any (e.g., migration barriers) to bull trout and other species that use tributaries to spawn.  Aggradation of deltas will be assess relative to flow conditions in the Kootenai River and tributaries if tributary discharges are available from MFWP and USFS monitoring efforts.  Annual surveys of the deltas will allow volumetric calculation of delta aggradation under known discharge conditions.

Objective 10.  Didymosphenia geminata monitoring will begin in the summer of 2009 to quantify the seasonality of blooms using dry mass and ash free dry mass as a measure of biomass.  Previous results indicated that 8 milligrams per square centimeter excluded shredders and scrapers from the invertebrate community.  Monthly samples will be collected from fixed sites from Libby Dam to the Fisher River confluence.

Objective 11.  Stable isotope analysis to assess the food web dynamics and energy flow of the Kootenai River downstream of Libby Dam to the Fisher River confluence.  Periphyton, invertebrate, and fish communities will be sampled throughout the year to assess seasonality of the food web and energy flow downstream of Libby Dam.

All Objectives in this statement of work require Environmental Compliance through BPA and scheduled data collection activities require Section 6 (bull trout) and or Section 10 (white sturgeon) consultation with the United States Fish and Wildlife Service prior to this  SOW and contract signing.  All sampling and tagging to be performed in this SOW are in categorical exclusions under BPA including installation of the remote PIT tag station in Quartz Creek, which was installed in 2007.  Coordination with project staff and staff in the Libby and Kalispell offices will be required for equipment use for items such as boats, electrofishing equipment, tagging equipment, tag readers, and telemetry equipment.  All existing long-term monitoring sampling designs have been previously designed, but new field work will require new sampling designs to be produced.  All data from fieldwork will be summarized depending on type of data and may include: population estimate, number of fish collected, length frequency histograms, weight-length relationships or relative weight calculations, species composition (%), dates of data collection, mean fish length by species, growth increments length, and results of model simulations for the physical and biological resources.  Statistical analysis will depend on what the data is used for and may include: calculation of a mean, standard deviation, standard error, 95% confidence interval, use of linear or non-linear regression analysis, and use of Analysis of Variance.