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, water released from Hungry Horse and Libby Dams was supposed to be limited to 10 feet from full pool (elevations 3550 and 2449, respectively) during the months of July through September 30 and during drought years, the draft could be increased to 20 feet from full pool by September 30.  However, the Mainstem Amendments have not been fully implemented to date.  The Mainstem Amendment dam operation strategy also stabilizes the release of water to the South Fork Flathead and Kootenai Rivers during the summer months (i.e., July through September).  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 HRMOD and LRMOD to calculate the amount of physical habitat available for aquatic productivity resulting from reservoir drafts in the Mainstem Amendments in Hungry Horse and Libby Reservoirs 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 1 uses Work Elements: D, O, P, Q, R

Objective 2.   Use HRMOD and 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 Hungry Horse and Libby Reservoirs.  Biological responses will be modeled in a similar fashion to the physical habitat in Objective 1, and utilize the same data files.  Objective 2 uses Work Elements: D, O, P, Q, R

Objective 3.   Compile age-growth and condition factor data from annual gill net series to compare actual growth at age (i.e., of kokanee and possibly other game fishes) under varying reservoir operating strategies to long-term composite growth increments.  Relate variation in growth increments to environmental and biological conditions. Spring (i.e., May) and Fall (i.e., September) gill net series will be set and used as an index of fishes abundance.  Length and weight data will be used to calculate relative weights for species with proposed or accepted standard weight equations.  Gill net data will also be used for collection age estimating structures (e.g., scales, fin rays / spines, otoliths) for game species and these will be used to calculate the annual growth increments by back calculating length at age and measuring the actual scale increment using Optimus software.  Historical gill net samples will be used for past growth increment data collection and analysis.  Objective 3 uses Work Elements: A. B, F, O, P, Q, R

Objective 4.   Update the Libby Reservoir (LRMOD) and Hungry Horse Reservoir (HRMOD) models using data from recent years to improve the predictive capability of the hydrologic model to better estimate the unregulated component of the flow via a regression on reservoir inflow.  Inflow discharge, outflow discharge, and water surface elevations will be collected for Hungry Horse and Libby Reservoirs for water years after initial model development, approximately 1996.  This may provide better model resolution and predictive capability of biological and physical impacts related to dam operations.  Objective 4 uses Work Elements: P, Q, R

Objective 5.   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 uses Work Elements: E, O, P, Q, R

Objective 6.  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 Flathead and Kootenai Rivers and associated tributaries.  Cohort survival will be assessed using data from annual population estimates (i.e., age frequency histogram) in the mainstem Kootenai and South Fork Flathead River and tributaries collected during the Spring, summer, and fall months.  Water quality (e.g., temperature and discharge data) will be obtained from the United States Army Corps of Engineers, from remote temperature loggers placed in specific tributaries, or taken in the field on a weekly basis where population estimate data are collected.  Fish (>250-300 mm) will be PIT tagged and if recaptured in subsequent years, may also provide information on survival and growth estimates under various biological and physical conditions.  Handling fishes also allows for collection of age estimation structure used in Objective 8.  Objective 6 uses Work Elements: A, B, C, G, O, P, Q, R

Objective 7.   Use radio telemetry to assess fish locations and movement associated with river flows and ramping rates.  Verify IFIM model simulations using radio telemetry in selected reaches in the Kootenai River below Libby Dam. Fish for radio telemetry will be collected via nighttime electrofishing efforts during population estimate surveys or during other electrofishing efforts.  Fish will be tracked via vehicle, boat, or fixed-wing aircraft on a weekly or bi-weekly basis below Libby Dam.  Fish locations (e.g., triangulated) will also be used to verify existing IFIM models of depth and velocity usage for bull trout and rainbow trout during day and nighttime hours.  The effects of sampling rates on fish movement will be assessed by calculating the average distance moved during periods of stable, increasing, or decreasing discharge periods.  Fish implanted with radio transmitters will not have the tag exceed 2% of their body weight.  Objective 7 uses Work Elements: A. B, C, G, I, O, P, Q, R

Objective 8.  Assess how dam operations and tributary conditions influence population demographics (i.e., growth, survival, life history, hybridization / genetics) of rainbow (RBT) and westslope cutthroat trout (WCT) populations in the upper Flathead River and growth and survival of juvenile and subadult bull trout in Trail Creek.  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 in the Kootenai River drainage.  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 >250-300mm to assess growth of known fishes 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) will be installed in Quartz Creek to assess how tributary biological and physical conditions affect migration patterns and spawning tributary use by adult fishes that have been tagged previously in the Mainstem Kootenai River.  The design of the remote PIT tag station will be obtained prior to equipment purchasing and provided to the equipment manufacturer, Biomark, Inc. located in Boise, Idaho.  Installation of equipment will require photo-documenting the installation site, and characterizing substrate sizes, channel sinuosity, bankfull width and depth measurements, water depth, and water velocities.  The remote PIT tag station must also be maintained on a weekly basis to monitor the power supply source (i.e., solar, battery, or propane) and replace or refill the needed power supply, remove any debris from the station, and may require removal of the station depending on habitat conditions such as low or high flow events or ice conditions.  Objective 8 uses Work Elements: A, B, C, G, H, J, K, L, N, O, P, Q, R

Objective  9. Compare length at age, growth increments, and condition of rainbow, westslope cutthroat and bull trout captured below Libby and Hungry Horse Dams via electrofishing to compare alternative system operation strategies.  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 uses Work Elements: A. B, C, G, H, O, P, Q, R

Objective 10.  Develop conservation theory and methods for effective application of risk-based monitoring of salmonid populations in the Flathead and Kootenai River drainages using Viable Population Monitoring.  Modeling efforts will use uredd count data and habitat use and movement data.  Objective uses work elements: A, B, M, O


All Objectives in this statement of work require Environmental Compliance through BPA and scheduled data collection activities required Section 6 consultation with the United States Fish and Wildlife Service prior to this FY2008 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, although additional permits were required with the United States Forest Service to install the station on federal lands.  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.