Selenium loads have been increasing over time in the Elk River, British Columbia, Canada, due to coal mining operations and runoff from associate spoil piles. The Elk River is a tributary to the Kootenay/Kootenai River and Lake Koocanusa. Extensive fish tissue monitoring has been conducted in Lake Koocanusa to assess the potential impacts of selenium from the Elk River (http://deq.mt.gov/DEQAdmin/LakeKoocanusa) However, fewer data are available for the Kootenai River downstream of Lake Koocanusa (downstream of Libby Dam). This 2018-2019 study generated baseline data on selenium and mercury concentrations in fish tissue and selenium and nutrient data in the water column of the Kootenai River and principal tributaries in Montana and Idaho. This data release is organized in two parts or "child items" for the fish tissue and water data, respectively. In addition to this compilation, the data are also being released through the USGS National Water Information System (NWIS) http://waterdata.usgs.gov/nwis/.