Concern has been raised that selenium contamination may be adversely affecting endangered fish in the upper Colorado River basin. The objective of the study was to determine if operation of a water control structure (opened in December 1996) that allowed the Colorado River to flow through a channel area at Walter Walker State Wildlife Area (WWSWA) would reduce selenium and other inorganic elements in water, sediment, aquatic invertebrates, and forage fish. Endangered Colorado pikeminnow were collected and muscle plug samples taken for selenium analysis. Selenium concentrations in filtered water were 21.0 ??g/L in 1995, 23.5 ??g/L in 1996, 2.1 ??g/L in 1997, and 2.1 ??g/L in 1998. Selenium concentrations in sediment cores and sediment traps were 8.5 ??/g in 1995, 8.2 ??g/g in 1996, 4.8 ??g/g in 1997, and 1.1 ??g/g in 1998. Selenium concentrations in aquatic invertebrates were 27.4 ??g/g in 1996, 15.5 ??g/g in 1997, and 4.9 ??g/g in 1998. Selenium concentrations in forage fish were 27.2 ??g/g in 1996, 20.2 ??g/g in 1997, and 8.6 ??g/g in 1998. Selenium concentrations in muscle plugs of Colorado pikeminnow were 9.8 ??g/g in 1995, 9.5 ??g/g in 1996, 9.0 ??g/g in 1997, and 10.3 ??g/g in 1998. Although selenium concentrations in water, sediment, aquatic invertebrates, and forage fish decreased substantially after operation of the water control structure, a corresponding change in Colorado pikeminnow did not seem to occur. Selenium concentrations in muscle plugs decreased with increasing fish total length and weight, did not change between repeat sampling in the same year or recapture in subsequent years, and seemed to be most closely associated with the mean monthly river flow for the March-July period. ?? 2004 Wiley Periodicals, Inc.