Nine stream sites in the Blackfoot River watershed in southeastern Idaho were sampled in September 2000 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 examined. Selenium was elevated in water, 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 water at eight sites (>5 ??g/L), sediment at three sites (>2 ??g/g), aquatic plants at four sites (>4 ??g/g), aquatic invertebrates at five sites (>3 ??g/g), and fish at seven sites (>4 ??g/g in whole body). The hazard assessment of selenium in the aquatic environment suggested low hazard at Sheep Creek, moderate hazard at Trail Creek, upper Slug Creek, lower Slug Creek, and lower Blackfoot River, and high hazard at Angus Creek, upper East Mill Creek, lower East Mill Creek, and Dry Valley Creek. The results of this study are consistent with results of a previous investigation and indicate that selenium concentrations from the phosphate mining area of southeastern Idaho were sufficiently elevated in several ecosystem components to cause adverse effects to aquatic resources in the Blackfoot River watershed. ?? 2004 Kluwer Academic Publishers.