Elevated selenium concentrations have been observed in several rivers in the western United States and are a concern for healthy aquatic systems. Water quality modeling is a valuable tool for quantifying the importance of sources and assessing management alternatives for stream standards compliance in basins with impaired water quality. This modeling study uses a relatively simple approach to describe a water distribution system and processes that drive loading of dissolved selenium and salts from the naturally occurring Cretaceous shale soils in the extensively irrigated Uncompahgre and Gunnison River Basins in Western Colorado. Calibrated model output characterizes processes that load an average total of 4,130 kg (9,100 lb) of selenium and 2.9× 108 kg (316,000 t) of salts per year from agricultural subbasins to the Uncompahgre River. Simulations of best management practices predict that extensive implementation of methods to minimize seepage and constituent loading would be required to reduce selenium c...