The California State Mussel Watch and the Regional Monitoring Program for Trace Substances have conducted biomonitoring for trace elements and organic contaminants in the San Francisco Estuary using transplanted bivalves (Mytilus californianus, Crassostrea gigas, and Corbicula fluminea). Significant declines (p<0.01) in contaminant concentrations in M. californianus for the period 1980–1996 were observed for PCBs, p,p′-DDE, cis-chlordane, dieldrin, and Ag, while a significant increase was observed for Cr (p<0.05). Certain limitations of the “mussel watch” approach are illustrated by examining data on survival, body condition, and contaminant uptake, including the inability of the technique to predict accumulation of mercury and selenium at higher trophic levels in the ecosystem. These results indicate that biomonitoring using transplanted bivalves, when part of a consistently supported long-term program, can produce valuable data on the spatially and temporally averaged abundance and distribution of certain contaminants in coastal ecosystems.