Nine stream sites in the Blackfoot River, Salt River, and Bear River watersheds in southeast Idaho, USA were sampled in May 2001 for water, surficial sediment, aquatic plants, aquatic invertebrates, and fish. Selenium was measured in these aquatic ecosystem components, and a hazard assessment was performed on the data. Water quality characteristics such as pH, hardness, and specific conductance were relatively uniform among the nine sites. Of the aquatic components assessed, water was the least contaminated with selenium because measured concentrations were below the national water quality criterion of 5 μ g/L at eight of the nine sites. In contrast, selenium was elevated in sediment, aquatic plants, aquatic invertebrates, and fish from several sites, suggesting deposition in sediments and food web cycling through plants and invertebrates. Selenium was elevated to concentrations of concern in fish at eight sites (> 4 μ g/g in whole body). A hazard assessment of selenium in the aquatic environment suggested a moderate hazard at upper Angus Creek (UAC) and Smoky Creek (SC), and high hazard at Little Blackfoot River (LiB), Blackfoot River gaging station (BGS), State Land Creek (SLC), upper (UGC) and lower Georgetown Creek (LGC), Deer Creek (DC), and Crow Creek (CC). The results of this study indicate that selenium concentrations from the phosphate mining area of southeast Idaho were sufficiently elevated in several ecosystem components to cause adverse effects to aquatic resources in southeastern Idaho.