After mostly freshwater replaced agricultural drainage water used for wetland management in 1985, Selenium (Se) concentrations in 3 wintering waterfowl species and black-necked stilts (Himantopus mexicanus) from the North and South Grasslands of central California, USA, declined in the years from 1986 to 1988 and 1989 to 1994. However, Se concentrations were still above the threshold for potential reproductive impairment and exceeded background levels for some species. Consequently, we measured Se concentrations in aquatic birds in 2005 after long-term use (20 yr) of predominately freshwater for wetland management in the Grasslands. As in 1986–1994, Se concentrations in 2005 were higher for birds from the South Grasslands, which historically received more undiluted drainage water compared with the North Grasslands. Liver Se concentrations for stilts from the South Grasslands were at levels associated with potential reproductive impairment. All species from the South Grasslands, as well as mallards (Anas platyrhynchos), northern pintails (A. acuta), and American coots (Fulica americana) from the North Grasslands, were above species-specific background levels. From 1994 to 2005, Se levels in some aquatic birds stabilized above background levels likely indicating long-term cycling within the Grasslands. We recommend Se-contaminated drainage water (≥2 ppb Se) not be used for management or allowed as an input into arid wetlands throughout the western United States.