The San Francisco Estuary, California, contains mercury (Hg) contamination originating from historical regional gold and Hg mining operations. We measured hydrological and geochemical variables in a tidal marsh of the Palo Alto Baylands Nature Preserve to determine the sources, location, and magnitude of hydrological fluxes of methylmercury (MeHg), a bioavailable Hg species of ecological and health concern. Based on measured concentrations and detailed finite-element simulation of coupled surface water and saturated-unsaturated groundwater flow, we found pore water MeHg was concentrated in unsaturated pockets that persisted over tidal cycles. These pockets, occurring over 16% of the marsh plain area, corresponded to the marsh root zone. Groundwater discharge (e.g., exfiltration) to the tidal channel represented a significant source of MeHg during low tide. We found that nonchannelized flow accounted for up to 20% of the MeHg flux to the estuary. The estimated net flux of filter-passing (0.45 μm) MeHg toward estuary was 10 ± 5 ng m–2 day–1 during a single 12-h tidal cycle, suggesting an annual MeHg load of 1.17 ± 0.58 kg when the estimated flux was applied to present tidal marshes and planned marsh restorations throughout the San Francisco Estuary.