Concentrations of Ag, Al, Cr, Cu, Fe, Hg, Mn, Ni, Pb, V and Zn were determined in six sediment cores from San Francisco Bay (SFB) and one sediment core in Tomales Bay (TB), a reference estuary. SFB cores were collected from between the head of the estuary and its mouth (Grizzly Bay, GB; San Pablo Bay, SP; Central Bay, CB; Richardson Bay, RB, respectively) and ranged in length from 150 to 250 cm. Concentrations of Cr, V and Ni are greater than mean crustal content in SFB and TB sediments, and greater than found in many other coastal sediments. However, erosion of ultramafic rock formations in the watershed appears to be the predominant source. Baseline concentrations of other metals were determined from horizons deposited before sediments were influenced by human activities and by comparing concentrations to those in TB. Baseline concentrations of Cu co-varied with Al in the SFB sediments and ranged from 23.7±1.2 μg/g to 41.4±2.4 μg/g. Baseline concentrations of other metals were less variable: Ag, 0.09±0.02 μg/g; Pb, 5.2±0.7 μg/g; Hg, 0.06±0.01 μg/g; Zn, 78±7 μg/g. The earliest anthropogenic influence on metal concentrations appeared as Hg contamination (0.3–0.4 μg/g) in sediments deposited at SP between 1850 and 1880, apparently associated with debris from hydraulic gold mining. Maximum concentrations of Hg within the cores were 20 times baseline. Greater inventories of Hg at SP and GB than at RB verified the importance of mining in the watershed as a source. Enrichment of Ag, Pb, Cu and Zn first appeared after 1910 in the RB core, later than is observed in Europe or eastern North America. Maximum concentrations of Ag and Pb were 5–10 times baseline and Cu and Zn concentrations were less than three times baseline. Large inventories of Pb to the sediments in the GB and SP cores appeared to be the result of the proximity to a large Pb smelter. Inventories of Pb at RB are similar to those typical of atmospheric inputs, although influence from the Pb smelter is also suspected. Concentrations of Hg and Pb have decreased since the 1970s (to 0.30 μg/g and 25 μg/g, respectively) and were similar among all cores in 1990. Early Ag contamination was perhaps a byproduct of the Pb smelting process, but a modern source of Ag is also indicated, especially at RB and CB.