Increased nutrient loading in aquatic environments can have a long-lasting influence on ecosystem processes and functions. The Kootenai River was historically oligotrophic, but nitrate levels have been steadily increasing since the mid-2000s, while phosphorus levels have remained low. Our study objective was to evaluate the current nutrient distribution throughout the Kootenai River watershed in the context of land use and land cover change. Each of the three land cover types we assessed, agriculture, developed areas, and surface mines, encompass less than 1% of the land area in the Kootenai River watershed. We measured nitrate, ammonium, and soluble reactive phosphorus (SRP) monthly at sites spanning 400 river km on the Kootenai River, and co-located tributary sites in British Columbia, Canada, and Montana and Idaho, USA. During July 2017, we measured the same nutrients along each of the selected tributaries with co-located sites at sub-catchment tributaries. Sites were selected to include a range of contributing drainage areas identified as agricultural, developed, or mining. Nutrient concentrations ranged from 0.012 to 4.