Project Background

In 2003, the Northwest Power and Conservation Council (Council) directed the Pacific Northwest region to implement and evaluate a new dam operating strategy at several 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 could 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) and have been in effect for 3 years.  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 the Mainstem Amendment operating strategy at Libby and Hungry Horse Dams, Montana.  The  Mainstem Amendments were  implemented in October 2008 and have been implemented for the past 3 water years.  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 modeling and field 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.

b.  Objectives

Montana Fish, Wildlife & Parks has 10 objectives in this SOW for evaluating the Council's prescribed  Mainstem Amendments on fisheries and habitat upstream and downstream of Hungry Horse and Libby Dams, Montana.  Some objectives have been completed in the past and were deleted from this SOW, while other new objectives have been added.  Some objectives 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 in the post Libby Reservoir period.  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 data for fishes in Libby Reservoir from annual gill net series to compare biological data under varying reservoir operating strategies.  Relate any variation  in growth, mean length at age, and condition 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 estimating annual growth increments.

Objective 4.   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  in Montana since the late 1970's.  The first 3 years of sampling has resulted in the capture of 13 white sturgeon.  Of these fish, most migrated upstream  from Idaho as opposed to being stocked into Montana.  Many of these movements began near or downstream of Bonners Ferry and these large upstream migrations had previously been undocumented during 20 years of radio and sonic tagging white sturgeon in Idaho and British Columbia in the Kootenai River system.  All of the captured white sturgeon were the result of hatchery efforts and no wild sturgeon have been captured in Montana between 2009 and 2011.  We will continue this sampling in 2012 to further assess the status of white sturgeon in Montana.  All data collected on captured white sturgeon will be sent to the Idaho Department of Fish and Game for inclusion in the shared Kootenai River white sturgeon database, which is used for estimating growth and survival of the species throughout the Kootenai River in Idaho, Montana, and British Columbia. Expansion of efforts including sonic tagging sturgeon captured in Montana using tags with 5-10 year life spans will allow assessments of long term residency and potentially identifying habitat use and spawning in Montana.

Objective 5.   Use Instream Flow Incremental Methodology (IFIM) and RIVBIO models quantify the amount of physical habitat occurring as a result of historic and recent dam 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 listed above and comparisons will be made on annual and seasonal levels. Assessments of discharge variation and water temperatures will also be made to assess impacts of changes to dam operations and any links to fish growth and conditions will be made where applicable..

Objective 6.  Estimate annual salmonid (i.e., Oncorhynchus spp.) cohort survival and relate annual survival estimates to environmental variables including discharge variation and peak discharge in the Kootenai River.  Cohort survival will be calculated using age frequency data collected during annual population estimates in the Kootenai  River.  Discharge and some water quality data (e.g., temperature and others) will be obtained from the United States Army Corps of Engineers and United States Geological Survey.  

Objective  7. Calculate and compile mean length at age, growth increments, and condition  of rainbow, westslope cutthroat, mountain whitefish, 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.   Recaptured fish with PIT tags will also be used for calculating annual growth increments and age estimates to validate cohort survival (see  Objective 6.)  

Objective 8.  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 by the USFS Canoe Gulch Ranger District 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 to download data.  

Objective 9.  Monitoring of the seasonal dynamics of Didymosphenia geminata blooms using previously developed indices such as periphyton thickness or percent coverage which were developed during monitoring efforts from 2009 to 2011.  Habitat conditions associated with blooms may also be measured.  Didymosphenia geminata is a nuisance diatom native to the pacific northwest and was present at nuisance levels for the first time in the Kootenai River in 2001. Previous research indicated that periphyton biomass ranging from 3-5 milligrams per square centimeter began to exclude shredders and scrapers from the invertebrate community. Biomass levels greater than 8 milligrams per square centimeter completely excluded them during the summer and fall months in the Kootenai River.  Data collected in 2009-2011 indicate that blooms are the most severe from February through May.  We will continue to monitor the percent coverage and thickness of blooms in the Kootenai River at the 20 established monitoring sites from Libby Dam to the Fisher River confluence using indices of thickness and percent coverage in conjunction with proposed experiments  being performed on the Kootenai River in the fall / winter of 2011-2012 by the USACE, KTOI, USGS, and the South Dakota School of Mines and Technology.  The experiments aim to test the effects of altered water quality and other parameters of a variety of aspects of Didymosphenia geminata. Information on the presence or absence of Didymospehnia geminata and biomass levels will also be collected in two additional sections of the Kootenai River, one near Libby, Montana and another near Troy, Montana in conjunction with Objective 10.

Objective 10.  Compile and summarize data on the aquatic invertebrate community  and fish diets in the Kootenai River, Montana to address any changes that have occurred since completion of Libby Dam such as trends in density, species composition, or other metrics reported.  Additional benthic aquatic invertebrate, fish diet, and benthic periphyton sampling will be completed in 2011-2012 in three different sections of the Kootenai River (i.e., Dam-Fisher, Flower-Pipe, and Troy) to assess if there are any differences in the benthic aquatic invertebrate community, fish diets, growth, and water temperatures to possibly identify limiting factors.  Bioenergetics may be used to assess which variable has the greatest impact on the fish population in terms of growth.  

Objective 11.  Assess vertical and lateral build up of deltas at bull trout spawning tributaries to the Kootenai River downstream of Libby Dam.

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 may 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 means, standard deviations, standard errors, 95% confidence intervals, use of linear , non-linear, and logistic regression analysis, and use of Analysis of Variance.