Lake Koocanusa was named in a contest won by Alice Beers of Rexford, Montana.

According to a March 8, 2021 article in The Narwhal, concerns have been raised about selenium pollution leaching from Teck Resources' Elk Valley open pit coal mines' waste rock, which is upstream from the lake system.

[3] A September 24, 2020 Montana Department of Environmental Quality presentation to the Board of Environmental Review Meeting, reported that the 95% of the selenium coming into Lake Koocanusa originates from the Elk River—"which has been contaminated by current and historic coal mining in the Elk Valley."

[5][6] In the spring of 2020, Teck Resources, had "reported a dramatic decline in adult westslope cutthroat trout in Elk Valley waterways closest to its mines".

[3] Since 2015, British Columbia and Montana have agreed to adopt aligned standards for selenium levels by 2020.