Spatial distributions of selenium were determined in fine-grained, oxidized, surface sediments and in two benthic bivalves (Corbicula sp., a suspension-feeding freshwater clam, and Macoma balthica, a deposit-feeding brackish-water clam) within San Francisco Bay, the San Joaquin River and three river systems unlikely to be subject to selenium inputs. Biologically available selenium enters the middle reaches of the San Joaquin River from agricultural runoff. However, selenium concentrations in sediments and Corbicula in the lower San Joaquin, upstream from San Francisco Bay, were not significantly different from concentrations in rivers with no known selenium inputs. Biologically available selenium did not appear to enter the northernmost reach of San Francisco Bay from the San Joaquin River in levels which could measurably influence bioaccumulation by Corbicula. Selenium concentrations in Corbicula were enriched in the northernmost reach of San Francisco Bay compared with the rivers, but several lines of evidence suggested that local inputs (perhaps from urban/industrial waste discharges) were the most important sources. Selenium concentrations in Macoma balthica were also elevated at one station in the northern reach of the Bay and at one station in the extreme South Bay. However, no enrichment was evident at two other stations, suggesting a lack of bay-wide contamination. No significant correlation between selenium and mercury concentrations in Corbicula tissues was observed.