NOTE TO CONTRACT OFFICER:  Send contract documents to Mike Burke, mburke@mt.gov.

Project Background
ws052548
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 12 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 resulting form changes to dam operations.

Objective 1.  Compile and summarize fish species composition, condition of various fish species, and CPUE of select fish species in Libby Reservoir.  Fish will be collected using annual spring and fall gillnet series to compare biological metrics under varying reservoir operating strategies and observed physical conditions.  

Objective 2.  Estimate annual and cohort survival rates of combined rainbow and cutthroat trout (i.e., Oncorhynchus spp.) in sections of the Kootenai River where population estimate and age frequency data are available.  Age validation from multiple sections will be completed in 2014 and will allow us to evaluate if age estimates from scales are reliable and for which age cohorts in which sections.  If reliable, estimated survival estimates will be related  to environmental variables including discharge variation, peak discharge, and monthly and seasonal discharge and other dam operation metrics.  Cohort survival will be calculated using age frequency data estimated from scales collected during annual population estimates in the Kootenai  River.

Objective  3. Calculate and compile condition and size structure of rainbow trout, westslope cutthroat trout, mountain whitefish, and bull trout captured downstream of Libby Dam.  Population estimates allow for the collection of length and weight data to assess condition and size structure indices which will be related to operation metrics including discharge variation, peak flows, water temperatures and other annual and seasonal metrics to assess which factors of dam operations affect condition of various species in the Kootenai River.

Objective 4.  Evaluate juvenile to adult survival of bull trout in Quartz Creek using PIT tag returns as well as survival estimates from an annual monitoring section.  A juvenile population estimate are completed annually in Quartz Creek and age frequencies will be calculated using length frequency data and estimated ages from length frequency information.  Juvenile to adult survival will be estimated using returns of PIT tagged juvenile bull trout from 2007-2013.  A remote PIT tag station was installed in Quartz Creek in August 2007 and is being used to detect returning adult and outmigrating juvenile PIT tagged bull trout between 2008 and 2017.

Objective 5.   Continue to assess the current status of white sturgeon in Montana as a supplemental effort to ongoing recovery, habitat restoration, monitoring, and aquaculture activities in Idaho.  Monitoring since 2009 in Montana resulted in the capture of 122 sturgeon, representing 81 individuals, and multiple age classes.  Approximately 98% of the captured sturgeon were of hatchery origin, but 2 wild sturgeon have been captured.  Some of the larger sturgeon are approaching sexual maturity and have had 5-10 year sonic tagged implanted to assess long term residency and movement, and to identify the potential for spawning sturgeon in Montana.  

Objective 6.  Continue to monitor of the seasonal dynamics of Didymosphenia geminata blooms using previously developed indices such as periphyton thickness and percent coverage and relate observed metrics to seasonal and annual dam operations.  Didymosphenia geminata is a diatom native to the northern hemisphere and nuisance mats appeared for the first time in the Kootenai River in 2001 despite being present since at least the late 1970's. Previous research indicated that periphyton biomass can exclude shredders and scrapers from the invertebrate community during the summer and fall months in the Kootenai River.  Data collected from 2009 to 2011 indicated that blooms were the most severe from February through April and mats could completely exclude shredders and scrapers.  We will continue to monitor percent coverage and thickness of mats of D. geminata in the Kootenai River at the 20 established monitoring sites from Libby Dam to the Fisher River confluence until ongoing experiments  being performed on the Kootenai River from 2013-2015 are completed.  Experiments are evaluating potential treatments to reduce / eliminate mat formation and addressing possible bloom mechanisms.  Identification of potential cost effective treatments will allow pre versus post treatment analysis to be performed following implementation of possible treatments,  If no treatments are identified, we will reevaluate the need to continue this work.

Objective 7.  Compile and summarize data on the aquatic invertebrate community in the Dam-Fisher section of the Kootenai River, Montana to assess annual variability in invertebrate metrics including density, species composition, % EPT, biomass, and others.  Annual changes in invertebrate metrics will be related to dam operations, periphyton metrics, and physical habitat conditions.  

Objective 8.  Assess catch rates, harvest rates, size structure of harvested fish, species composition of the catch, angler demographics, and angler effort on the Kootenai River downstream of Libby Dam and compare to previous estimates.  A secondary part of this creel survey is to assess angler attitudes towards the current status of the Kootenai River, habitat conditions, and possible limiting factors and may include current dam operations, regulations, limiting factors, and potential mitigation efforts.  

Objective 9.  Monitor D. geminata in the Flathead River

Objective 10.  Estimate juvenile to adult survival of bull trout in tributaries of the Flathead River

Objective 11.  Assess angler effort, catch, and harvest on the Flathead River

Objective 12.  Assess aspects of mountain whitefish in regulated and unregulated portions of the Flathead 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.  Maintenance of the PIT tag stations may require additional permits.  Coordination of staff in the Libby and Kalispell offices may be required for some work elements.  All existing long-term monitoring sampling designs have been previously designed, but new field work may require new sampling designs to be produced or use common design for those types of data collection.  

All data from fieldwork will be summarized depending on type of data and may include: population estimates, 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, invertebrate metrics, angler effort, harvest, and catch rates, and summaries of dam operations including reservoir inflow, outflow, elevation, and water temperature.  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 Analysis of Variance with post-hoc tests.