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 in Montana 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.   The Mainstem Amendment dam operation strategy also stabilizes water released into the South Fork Flathead and Kootenai Rivers by implementing hourly and daily limits on how quickly discharges can be increased or decreased on a seasonal basis.  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.  The Mainstem Amendments were officially implemented in October 2008 (i.e., water year 2009).  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.  Historical river discharges and reservoir elevations, modeled physical habitat and biological conditions, gill netting data, and lotic fish population estimate data will provide an environmental baseline for comparison to 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  implemented in October 2008.  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.  The new operation strategy limits the summer drafts of Libby Reservoir (Lake Koocanusa) 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% (i.e, drought) of water supply years.  The Mainstem 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 operations will stabilize flow in the rivers during the productive summer months, while meeting established minimum flow requirements for species such as bull trout and providing tiered flows in the spring for Kootenai River white sturgeon.  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 upstream and downstream of Libby and Hungry Horse Dams, Montana.

b.  Objectives

Montana Fish, Wildlife & Parks has eleven objectives for evaluating the Council's prescribed  Mainstem Amendments on fisheries and habitat upstream and downstream of Hungry Horse and Libby Dams, Montana in FY2006.  Some objectives have already been completed and others have been added and 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 model the physical habitat conditions occurring in Libby Reservoir as a result of the Mainstem Amendment operating strategy and compare current conditions to previous physical conditions.  Model simulations will be run using historical and recent Kootenai River inflow, outflow, and reservoir surface elevation data collected by the United States Geological Survey and the United States Army Corps of Engineers.

Objective 2.   Use LRMOD to calculate the biological responses (e.g., biological production of benthos, invertebrates, zooplankton, primary production) resulting from the Mainstem Amendments at Libby Reservoir and compare results to prior operating strategies.  Biological responses will be modeled in an identical fashion to the physical conditions in Objective 1 and utilize the same input data files.  

Objective 3.   Calculate and 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 netting will also permit collection of age estimating structures (e.g., scales and otoliths) for game species and these will be used to estimate ages of fishes and digitize annual growth increments.

Objective 4.   Use Instream Flow Incremental Methodology (IFIM) and RIVBIO models to model the amount of physical habitat occurring as a result of historic and recent operating strategies in the Kootenai River for  juvenile and adult rainbow and bull trout.  Model simulations will use the same outflow discharge files as Objectives 1 and 2.

Objective 5.  Estimate annual salmonid (i.e., Oncorhynchus spp.) cohort survival and relate annual survival estimates to environmental variables including discharge variation and peak discharges  in the Kootenai River.  Cohort survival will be calculated using age frequency data collected during annual population estimates in the Kootenai  River.  Water data (e.g., temperature and discharge data) will be obtained from the United States Army Corps of Engineers and United States Geological Survey.  

Objective  6. Calculate and compile length at age, growth increments, and condition data 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 (e.g., scales and otoliths) and length and weight data.   Fishes that have been injected with PIT tags will also be used for calculating annual growth increments.  

Objective 7.  Evaluate how tributary conditions (e.g., discharge and temperature) affect growth, survival, migration patterns, and spawning tributary use of bull trout in Quartz Creek.  Juvenile population estimates are completed in Quartz Creek annually using depletion techniques (2-3 downstream passes; reach length 150m) until a 70% depletion efficiency is achieved between consecutive passes.  Age frequencies will be calculated using length frequency data and from estimated ages from scales collected during electrofishing surveys.  Discharge and water temperature will be collected using measured discharges calibrated to a staff gage and temperature loggers deployed throughout the Quartz Creek drainage.  Survival and mortality estimates will be related to the biological (e.g., population density, size structure) and physical parameters (e.g., temperature, discharge).  PIT tags will  be injected  into fish >100mm to assess growth, migration patterns, and returns of outmigrating juvenile bull trout as adults.  A remote PIT tag station was installed in Quartz Creek in August 2007 to detect PIT tagged fishes which will help assess how tributary conditions (e.g., discharge, temperatures) affect migration patterns of juvenile and adult bull trout.   The remote PIT tag station array records the date, time, and direction of each PIT tag detected and must be maintained on a regular basis (2-4 times per month) to monitor the power supply, remove any debris from the station, and downloading data.  

Objective 8.   A pilot sampling project began in the summer of 2009 to assess the current status of white sturgeon in Montana.  White sturgeon have been stocked into the Montana portion of the Kootenai River since 1994 but no sampling has occurred to assess the status, survival, growth, or abundance of the species in Montana since the late 1970's.  The initial 2009 sampling season resulted in the capture of two white sturgeon in Montana.  Both of the captured white sturgeon were stocked into the Kootenai River from the Kootenai Tribe of Idaho hatchery in Bonners Ferry, Idaho.  All data collected on captured white sturgeon will be sent to the Idaho Department of Fish and Game for inclusion in the Kootenai River white sturgeon database.

Objective 9.  Survey the deltas of six primary spawning tributaries (i.e, Callahan Creek, O'Brien Creek, Quartz Creek, Pipe Creek, Libby Creek, and Fisher River) of bull trout to assess the potential impacts (e.g., aggradtion, formation, barriers) to bull trout and other species that use these tributaries to spawn.  Aggradation of deltas will be assessed relative to flow conditions in the Kootenai River and tributaries where possible.  Annual surveys of the deltas will allow volumetric calculation of delta aggradation and changes in the streambed elevation for comparison to historical delta surveys.

Objective 10.  To quantify the seasonality of Didymosphenia geminata blooms using ash free  dry mass (AFDM) and to assess the habitat conditions associated with increased biomass.  Didymosphenia geminata is a nuisance diatom native to the pacific northwest and was present at nuisance levels in the Kootenai River in 2001. Previous research indicated that 3-5 milligrams per square centimeter began to exclude shredders and scrapers from the invertebrate community and levels greater than 8 milligrams per square centimeter completely excluded them during the summer months in the Kootenai River.  An index for rapid assessment of AFDM conditions may be developed using 2009-2010 data and if possible will be used during this contract period to assess the biomass of the periphyton community.  

Objective 11.  Stable isotope analysis will be used to assess the food web dynamics and energy flow of the Kootenai River downstream of Libby Dam to the Fisher River confluence.  Invertebrate and fish communities will be sampled throughout the year to assess seasonality of the food web and energy flow downstream of Libby Dam.  This work will be linked to data in Objective 10 if possible to quantify the impacts of the periphyton community on the food web of the Kootenai River.

All Objectives in this statement of work require Environmental Compliance through BPA and scheduled data collection for fishes require Section 6 (bull trout) and 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.