38 I NTRODUCTION T race metals can be an influential factor in ecosystem processes, affecting the well-being of organisms, populations, and communities (Luoma 1996). Metal bioaccumulation in tissues of clams and other bottom dwelling organisms is an indicator of metal exposures that can either degrade the health of the organism, or be transferred up the food web to potentially harm higher organisms. It is critical to understand the interaction between ecosystem processes and the bioaccumulation of metals to begin to evaluate the metals’ importance in the ecosystem. Ecosystems are complex and variable. Environmental factors such as hydrology, water chemistry, sediment characteristics, and food availability fluctuate widely from year-to-year in estuaries and affect interpretation of pollutant influences. Yet on the time scale of a decade or more, consistent increases or decreases over time in the environmental factors are rare. If effects of pollutant exposure are imposed on this system, they cannot be separated, convincingly, in a few years of sampling. However, if pollutant inputs are declining over time, as has happened often in the United States since the passage of the Clean Water Act in 1972, the downward trend in exposure may be the only long-term trend in the data. So even though variability can create difficulty in understanding processes in a complex estuary such as San Fran- cisco Bay, it can also provide opportunities to examine the factors that influence accumulation of metals in estuarine species. This article describes work performed under the US Geological Survey Toxic Substances Hydrology Program, which is unique among Lessons Learned About Metals in the Estuary: The Importance of Long-term Clam Accumulation Data Cynthia L. Brown (clbrown@usgs.gov), Samuel N. Luoma, Francis Parchaso, and Janet K. Thompson, U.S. Geological Survey Key Points • Natural variability can create difficulty in under- standing processes in a complex estuary such as San Francisco Bay, it can also provide opportunities to examine the factors that regulate accumulation of metals in estuarine species • Freshwater inflow is a primary influence on accumulation of some metals • Silver concentrations have declined significantly in the South Bay, with the greatest declines occur- ring in the 1980s, before the RMP began its sam- pling • Evidence strongly points to silver (perhaps in combination with copper) as a potential disrupter of clam reproduction at concentrations well below those typically used in toxicity tests