The New Almaden mercury mines in California (USA), which collectively represent the largest historic producers of mercury in North America, are a persistent source of mercury contamination to the San Francisco Bay estuary. An estimate based on total mercury concentration (HgTOT) and provisional stream flow data measured at a gauging station in the Guadalupe River during base flow conditions yields a base flow flux of 30 g of mercury for the month of October 2000. In contrast to this base flow estimate, one 2-day rain event in October 2000 resulted in a flux of 22 g of mercury past this site. An estimate of mercury transport from the entire Guadalupe River watershed based on a sediment transport model and our measured suspended particulate HgTOT (0.5–4 μg g−1) results in a total of 4–30 kg year−1 transported to the southern reach of the estuary. Sediments in the southern reach have lower HgTOT (most ≤0.4 μg g−1 dry wt) and monomethylmercury (MMHg, c. 1 ng g−1 dry wt) concentrations than those in the Guadalupe River (HgTOT, 0.41–33 μg g−1 dry wt; MMHg, 1–10 ng g−1 dry wt). Because the most elevated methylmercury concentrations (8–12 ng g−1 dry wt) were found in sediments deposited immediately upstream of hydraulic structures (e.g. diversion dams and weirs) within the river, it is proposed that such physical structures may represent important zones of MMHg production and fluxes to San Francisco Bay.