Assessing the impacts of mining in the Transboundary Flathead and Kootenai River systems

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The Transboundary Flathead and Kootenai Basins in Montana and British Columbia host some of the most diverse and unique native aquatic ecosystems throughout North America. Headwaters of these basin feed into Waterton-Glacier International Peace Park (U.S. and Canada) and Flathead Lake, and Lake Koocanusa and the Kootenai River in the U.S.   Despite the tremendous historical and ecological value of the region, the headwaters in the Flathead were targeted for coal mining, which may threaten water and habitat quality, migratory fish populations, and aquatic life downstream. A history of coal mining and coalbed methane extraction in the headwaters of the Elk River, which drains into Lake Koocanusa, suggest that upstream land use practices are producing sediment and water pollution that degrade waters downstream. Since 2008, the USGS has led an aquatics research project, working with Federal, State, and International partners, to help understand the effects on species and aquatic ecosystems and to provide information to support of the Transboundary Flathead and Kootenai Ecosystems.

Map of hte Elk River Ares in the Transboundary Flathead and Kootenai River Systems.

Map of hte Elk River Ares in the Transboundary Flathead and Kootenai River Systems.Public domain

Flathead: The North Fork Flathead River, which flows across the US-Canadian border just over the divide from Waterton-Glacier International Peace Park, is recognized as a regional stronghold for migratory bull trout and westslope cutthroat trout throughout their native range. Extensive studies have shown that a majority of their spawning and rearing occurs in the upper reaches of the Flathead River in Montana and British Columbia (BC). However, despite the importance of these critical habitats and native fish populations, the headwaters portion of the drainage was proposed for coal, gas and oil development.

For most of the perennial streams in BC and Glacier National Park, there is little information on water quality, fish distributions and genetic status of native populations, including the federally listed threatened bull trout and state sensitive westslope cutthroat trout. Additionally, limited information exists regarding the population genetic structure of migratory fish populations in the upper Flathead system. This project is designed to collect fish distribution, abundance and genetic information for many streams on the west side of Glacier National Park and the BC portion of the drainage. These data will be critical to document the current status of native fish population and critical spawning and rearing habitats prior to potential mining or other development of this drainage. This is a cooperative research and monitoring project with the USGS-NOROCK; Montana Fish; Wildlife and Parks; University of Montana; Montana Department of Natural Resources and Conservation; BC Ministry of Environment; and the Ktunaxa (too-nah-hah) First Nation of Southeast British Columbia to manage a shared transboundary fisheries and river system. 


The Transboundary Kootenai River Basin, which contains Lake Koocanusa, is one of the most treasured watersheds in the northwestern United States. It contains critical habitat for the threatened bull trout, genetically pure westslope cutthroat, and endangered white sturgeon. The river basin also serves a vital role in maintaining adequate flows and water quality for several endangered salmon and steelhead runs in the Columbia River. Historic and ongoing coal mining in the headwaters have degraded water quality within watershed. The Montana Department of Environmental Quality (MT DEQ) has identified Lake Koocanusa as threatened by selenium (Se) and listed the water body under Section 303 (d) of the US Clean Water Act. Se is an essential dietary element; however, it can be highly toxic to fish and aquatic birds when bioaccumulated in ecosystems, resulting in local extinctions and deformities.

Based on data compiled by the USGS and MT DEQ, annual Se loads entering Lake Koocanusa from the Elk and Fording rivers in Canada have increased from 2,600 kg in 1992 to over 13,000 kg in 2012, representing more than a 5-fold increase over 20 years. Water-quality monitoring results from Lake Koocanusa during 2015 indicated Se concentrations consistently exceeded 1 mg/L and periodically exceeded the U.S. Environmental Protection Agency’s proposed draft aquatic life ambient water quality criteria for Se in lakes and reservoirs of 1.2 mg/L (30-day average) (USEPA, 2015). Data from the Elk River in the headwaters suggest that sediment and water pollution from mining activities has degraded water quality and impacted aquatic biota downstream (Hauer and Sexton, 2013; FWP unpublished data), thus impacting the Transboundary Kootenai River Basin. Significant investigations into aquatic effects of Se have been conducted in the Elk River; however, adequate study of current and projected impacts to fish, birds, and wildlife has not been conducted in Lake Koocanusa.

Working within the framework of the Lake Koocanusa Monitoring and Research Working Group, this project includes development of: (1) information to support the development of a site-specific water-quality standard for Se using ecosystem scale modeling to ensure adequate protection of key threatened/native fish species in Lake Koocanusa under current and future Se loading and reservoir assimilation capacities; and (2) watershed and reservoir models to estimate and monitor Se and nitrate (derived from explosives residue) loads entering and leaving the reservoir as well as estimating the concentration of these constituents within the reservoir during ongoing reclamation activities.


Collaborators: Numerous federal, state, tribal, and local agencies are working to assess impacts to this watershed and include the USGS Montana/Wyoming Water Center (Dr. David Naftz), University of Montana (Dr. Ric Hauer), Confederated Salish and Kootenai Tribes (Erin Sexton); Ktunaxa Nation Council; U.S. Environmental Protection Agency; U.S. Fish and Wildlife Service; U.S. State Department; State of Montana (MT DEQ and Fish, Wildlife, and Parks); Army Corp of Engineers; Lincoln County; and BC Ministry of Environment.