Monitoring sediment quality and total mercury concentrations over the period 1993-2001 at 26 stations in San Francisco Estuary has shown the seasonal cycling of mercury sediment concentrations, as well as a significant (P < 0.05) decrease in those concentrations at eight stations across the estuary. This decrease in sediment mercury concentrations is attributed to the transport of relatively cleaner sediment to the estuary from the Sacramento River and San Joaquin River watersheds. Despite the decreases observed in some parts of the estuary, no corresponding trend has been found in concurrent studies on sport fish and bivalves in the estuary.