Widespread sediment toxicity has been documented throughout the San Francisco Estuary since the mid-1980s. Studies conducted in the early 1990s as part of the Bay Protection and Toxic Cleanup Program (BPTCP), and more recently as part of the Regional Monitoring Program (RMP) have continued to find sediment toxicity in the Estuary. Results of these studies have shown a number of sediment toxic hotspots located at selected sites in the margins of the Estuary. Recent RMP monitoring has indicated that the magnitude and frequency of sediment toxicity is greater in the winter wet season than in the summer dry season, which suggests stormwater inputs are associated with sediment toxicity. Additionally, spatial trends in sediment toxicity data indicate that toxic sediments are associated with inputs from urban creeks surrounding the Estuary, and from Central Valley rivers entering the northern Estuary via the Delta. Sediment toxicity has been correlated with a number of contaminants, including selected metals, PAHs and organochlorine pesticides. While toxicity identification evaluations (TIEs) suggest that metals are the primary cause of sediment toxicity to bivalve embryos; TIEs conducted with amphipods have been inconclusive.