San Francisco Bay is one of the world's largest urbanized estuarine systems. Its water and sediment receive organic input from a wide variety of sources; much of this organic material is anthropogenically derived. To document the spatial and historical record of the organic contaminant input, surficial sediment from 17 sites throughout San Francisco Bay and sediment cores from two locations Richardson Bay and San Pablo Bay were analyzed for biomarker constituents. Biomarkers, that is, 'molecular fossils', primarily hopanes, steranes, and n-alkanes, provide information on anthropogenic contamination, especially that related to petrogenic sources, as well as on recent input of biogenic material. The biomarker parameters from the surficial sediment and the upper horizons of the cores show a dominance of anthropogenic input, whereas the biomarker profiles at the lower horizons of the cores indicate primarily biogenic input. In the Richardson Bay core the gradual upcore transition from lower maturity background organics to a dominance of anthropogenic contamination occurred about 70-100 years ago and corresponds to the industrial development of the San Francisco Bay area. In San Pablo Bay, the transition was very abrupt, reflecting the complex depositional history of the area. This sharp transition, perhaps indicating a depositional hiatus or erosional period, dated at pre-1952, is clearly visible. Below, the hiatus the biomarker parameters are immature; above, they are mature and show an anthropogenic overlay. Higher concentrations of terrigenous n-alkanes in the upper horizons in this core are indicative of an increase in terrigenous organic matter input in San Pablo Bay, possibly a result of water diversion projects and changes in the fresh water flow into the Bay from the Delta. Alternatively, it could reflect a dilution of organic material in the lower core sections with hydraulic mining debris.