The study, commissioned by Glacier National Park, compared water quality in the Elk River with the neighbouring Flathead River basin.
Selenium levels were 10 times higher in the Elk River, and there were also increased levels of nitrogen and sulphate.
Selenium is a metal found in natural deposits, such as ores, and can end up in bodies of water when discharged from refineries and mines.
The study attributed the high levels of selenium to the five coal mines in the Elk Valley, which is considered a wildlife corridor and a hotspot for biodiversity.
John Barganske, executive director of Wildsight, an environmental organization in the Kootenays, said high levels of selenium could eventually lead to a total collapse of the Elk River fishery.
"This has been accumulating," he said. "It's not just a matter of it flows and it's gone. The levels continue to go up and up."
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