In order to understand the biogeochemistry of mercury in the San Francisco Bay estuary, California, we undertook a 2-year study of sediments and surface water's to investigate sources of mercury to the estuary and the processes that control its distribution. Over several seasons, unfiltered and filtered (< 0.45 mum) surface water samples were collected from 26 sites in the estuary and analyzed for total mercury (Hg-T) monomethylmercury (MMHg), and ancillary water quality parameters. Concentrations of mercury in unfiltered surface water UHgT ranged from 0.73 to 440 pM, and were well correlated with suspended particulate matter (SPM). Concentrations of UHgT were typically highest in the winter and spring, when precipitation, fluvial discharges, and SPM were greatest. Although the concentrations Of UHgT appear elevated with respect to other contaminated estuaries, this is largely explained by the high SPM in this system. The average concentration of mercury in suspended particles was 1.8 +/- 0.6 nmol g(-1), and was similar to the concentration of HgT in sediments (1.1 +/- 0.7 nmol g(-1)), especially when normalized to grain size (% < 63 mum; 1.7 +/- 0.7 nmol g(-1)), demonstrating the preferential resuspension of fine-grained sediment, and the importance of wind and tidal driven resuspension. in controlling UHgT concentrations. Concentrations of dissolved gaseous mercury averaged 0.90 +/- 0.88 pM, and the estuary was a net source of mercury to the atmosphere of 40-240 kg year(-1). The concentrations of surface water MMHg ranged from < 0.050 to 2.3 pM, and appeared to be controlled by input from the Sacramento-San Joaquin delta in the northern reach and by wastewater inputs in the extreme southern reach. Sediment mercury concentrations were significantly correlated with the fraction of fine-grained material present and the concentrations of total organic carbon. Concentrations of MMHg in the sediments ranged from 0.5 to 5.0 pmol g(-1), with an average of about 2 pmol g(-1); the highest concentrations were found in areas with detectable pore water sulfide, high nutrient input from wastewater, and low salinity. Although the mercury in this system is principally attributed to contamination from historic mining activity, concentrations were similar to those of other large, urbanized estuaries that are primarily contaminated with recent industrial inputs. (C) 2002 Elsevier Science B.V. All rights reserved.