The transboundary Koocanusa Reservoir (KR) encompasses the headwaters of the Kootenay (Kootenai - U.S.) watershed, a unique basin that crosses the U.S./Canadian border three times. KR receives waters enriched in Selenium (Se) from coal mines in the Elk River watershed, its second largest tributary. Se is necessary for life, but concentrations above essentiality can cause deformities, and mortality. Critical to understanding Se impacts on ecosystems and water-quality, is a need to understand how Se concentrations change in space and time. Water-quality degradation from increasing Se has been documented in KR and downstream; however, the magnitude and extent are not well understood. We used two approaches to track how Se concentrations have changed historically and persist downstream. First, we examined trends in flow-normalized concentrations and loads of Se for the Kootenay and Elk Rivers where they enter the KR, to understand historical changes entering the system. Second, we used seasonal-Kendell trends in Se concentrations, examining six locations in the Elk, Kootenai, and Upper Columbia Rivers for evidence of long-range transport. Trends entering KR from the Elk show unprecedented, large increasing trends (443% load, 551% concentration) spanning four decades, while the Kootenay showed a slight decrease. The Elk now contributes 95% of Se entering KR from these two major tributaries. Seasonal Kendall trends show consistent, increasing patterns, with dilution, suggesting Se persists over 400 miles downstream and through two large reservoirs (Koocanusa and Kootenay). These analyses illustrate unprecedented increase and persistence of Se throughout the upper Columbia River Basin from coal mining.