The Grassland Bypass Project, which began operation in September 1996, was conceived as a means of diverting brackish selenium-contaminated agricultural drainwater away from canals and sloughs needed for transporting irrigation water to wetlands within the Grassland Water District (the Grasslands), Merced County, California. The seleniferous drainwater is now routed into the San Luis Drain for conveyance to North Mud Slough and eventual disposal in the San Joaquin River. The purpose of this study was to determine the extent to which the Grassland Bypass Project has affected fishes in sloughs and other surface waters within and downstream from the Grasslands. During September-October 1997, 9,795 fish representing 25 species were captured at 13 sampling sites. Although several species exhibited restricted spatial distributions, association analysis and cluster analysis failed to identify more than one fish species assemblage inhabiting the various sites. However, seleniferous drainwater from the San Luis Drain has influenced selenium concentrations in whole fish within North Mud Slough and the San Joaquin River. The highest concentrations of selenium (12-23 ??g/g, dry weight basis) were measured in green sunfish Lepomis cyanellus from the San Luis Drain where seleniferous drainwater is most concentrated, whereas the second highest concentrations occurred in green sunfish (7.6-17 ??g/g) and bluegills Lepomis macrochirus (14-18 ??g/g) from North Mud Slough immediately downstream from the drain. Although there was some variation, fish in the San Joaquin River generally contained higher body burdens of selenium when captured immediately below the mouth of North Mud Slough (3.1-4.8 ??g/g for green sunfish, 3.7-5.0 ??g/g for bluegills) than when captured upstream from the mouth (0.67-3.3 ??g/g for green sunfish, 0.59-3.7 ??g/g for bluegills). Waterborne selenium was the single most important predictor of selenium concentrations in green sunfish and bluegills, as judged by results from multiple-regression analyses. Among bluegills, water temperature also contributed to the prediction of selenium body burdens.