The overarching goal of project 1994-049-00 is to recover a productive, healthy and biologically diverse Kootenai River ecosystem, with emphasis on native fish species rehabilitation. It is designed to aid the recovery of important fish stocks, i.e. white sturgeon, burbot, bull trout, kokanee and other salmonids important to the Kootenai Tribe of Idaho and regional sport-fisheries.  

The major objective of the project has been to address factors limiting key fish species within an ecosystem perspective. Major components completed include: establishment of a comprehensive and thorough biomonitoring program, investigation of ecosystem-level productivity, testing the feasibility of a large-scale Kootenai River nutrient addition experiment, evaluation and rehabilitation of key Kootenai River tributaries important to the health of the Kootenai River ecosystem, provision of funding for Canadian implementation of nutrient addition and monitoring in the Kootenai River ecosystem (Kootenay Lake) from lost  productivities created by construction and operation of Libby Dam, providing written summaries of all research activities, and, holding an annual workshop with other agencies to discuss management, research, and monitoring strategies related to this project and providing a forum to coordinate and disseminate data with other projects involved in the Kootenai River basin.    

The proposed biological objectives include : continuation of a system-scale multi trophic-level biomonitoring and water quality program sensitive to changes in biological  productivity,  continued evaluation and rehabilitation of key Kootenai River tributaries important to the health of the Kootenai River ecosystem, provision of funding for Canadian implementation of nutrient addition and monitoring in the Kootenai River ecosystem (Kootenay Lake), holding an annual meeting to convene with other agencies and institutions to discuss management, research, and monitoring strategies for this project and disseminate information, and, providing written summaries of all research  activities related to the project.  

Therefore this project, which addresses system productivity and other ecosystem level management issues (e.g. restoring normative flows as part of hydro operations), is crucial to recovery of the Kootenai River ecosystem in the post-Libby Dam era.

Problems Project Addresses:

The Kootenai River aquatic ecosystem has been significantly degraded due to wetland loss and impoundment during the last century causing nutrient deficiencies and reductions in habitat types and complexity. Very low levels of phosphorous and nitrogen have been found downstream of Libby Dam resulting in oligotrophic and ultra-oligotrophic conditions in most reaches. Chlorophyll a levels, macroinvertebrate, and salmonid densities are well below similar-sized regional rivers. Macroinvertebrate biomass, diversity, and fish condition factors are low and generally decline with increased distance from Libby Dam (Holderman and Hardy 2004). Kootenai River white sturgeon (Acispenser transmontanus ), burbot (Lota lota) and all salmonid species (Oncorhynchus spp.), important to Kootenai Tribal and regional sport fisheries, are scarce relative to historical accounts and are currently unfishable.

This project (199404900) is designed to address ecosystem level problems within a adaptive management framework. Currently system productivity in the regulated mainstem of the Kootenai River has been identified as a strong limiting factor to biogenic development in the river, ultimately resulting in reduced fisheries (KRSA 2004; Holderman and Hardy 2004). The International Kootenai River Ecosystem Team (IKERT) recommended in 2003 to initiate a 5 year experimental nutrient restoration effort, which began in July of 2005 with additions of liquid phosphorus to the Kootenai River near the Idaho-Montana border. However, additional problems remain. Most notable are a lack of habitat complexity (especially in the meander reach downstream of Bonners Ferry, ID, and key Idaho tributaries), and regulated flow patterns that are often at odds with the "natural" hydrograph that occurred prior to the construction of Libby Dam in 1972.

How this SOW Addresses Objectives:

This SOW addresses the aforementioned objectives in several ways. The biomonitoring work (monitoring of water quality and biologic trophic levels) is designed to characterize the ambient conditions in the Kootenai River, and provide a template of comparison for current and future restoration work within the basin (an exception to this is the fine-scale monitoring associated with the nutrient restoration in the main stem Kootenai River. This work is designed to directly monitor the effects of nutrient additions and provide data to finely tune and evaluate the project, and, meet state and federal water quality compliance standards). SOW work elements concerning nutrient restoration in Kootenay Lake and river are addressing biological productivity issues that have been identified in the Kootenai River Sub Basin Plan (KRSBP 2004). The river fertilization work is designed to replace limiting nutrients lost within Libby Reservoir, and boost primary productivity in the Idaho reach of the river, ultimately resulting improved fisheries (eg. more rainbow trout per mile; improved sturgeon growth and condition, improved forage base for all fish species). Tributary riparian restoration work addresses habitat needs that will benefit resident fish species, such as kokanee, rainbow trout and burbot, all species that play important roles in the Kootenai River ecosystem. Kokanee provided a seasonal food source for white sturgeon, and cycled nutrients from Kootenay Lake back to Idaho tributaries in quantities that likely had a significant effect on stream productivity, which in turn benefited resident salmonids and juvenile burbot. Kootenay Lake nutrient work is designed to benefit kokanee, sturgeon, trout and burbot stocks in the South Arm of the lake. All these species make annual spawning migrations to Idaho streams that fed the Kootenai River. Thus the nutrient restoration work in Kootenay Lake, British Columbia, tributary habitat restoration in Idaho, main stem fertilization, and other aspects of this project are designed to compliment one another.

Kootenai Tribe Working in coordination with the British Columbia Ministry of Environment to plant eyed kokanee eggs in tributaries to the Kootenai River and Kootenay Lake.
The South Arm of Kootenay Lake kokanee escapements were virtually non-existent and did not responded to North Arm fertilization though the North Arm kokanee stock did. A review of the historical data supports the notion that larger South Arm escapements were evident, at least in the low thousands, 3-4 decades ago. Today they are in the low hundreds.  The same trend is evident for escapement data summarized for North Idaho streams that flow into the lower Kootenai River.  The 2006 stream counts in British Columbia and Idaho indicated that only a few fish (most < 25) were present in several streams.  By 2012, however, kokanee spawners increased to several thousand in the south arm Kootenay Lake streams in British Columbia and northern Idaho indicating that nutrient augmentation, along with habitat improvements are working to improve kokanee numbers.

With recent implementation of nutrient enhancement in the South Arm of Kootenay Lake, eyed kokanee egg plants in the South Arm tributaries will produce kokanee fry that benefit from South Arm fertilization and restore South Arm kokanee runs.