Five field trips were conducted in the San Francisco Bay-Delta between May 2000 and October 2001 to investigate the sediment-water exchange of total mercury (Hg) and monomethyl mercury (MMHg). Solid-phase Hg averaged ϳ1 nmol g Ϫ1 and did not show any variability with depth or time or among sites. In contrast, solid-phase MMHg showed considerable vertical, temporal, and spatial variability (0.4-66 pmol g Ϫ1 ), with the highest values occurring at a peat-rich environment in May 2001, suggesting that MMHg production was largely controlled by temporal factors and habitat type. In pore water, both Hg and MMHg concentrations were generally elevated near the sediment-water interface during warm months. Sediment-water exchange flux of MMHg, determined with benthic chamber deployments, ranged from Ϫ92 to 850 pmol m Ϫ2 d Ϫ1 , with higher values occurring in May. In most cases, diffusional fluxes of Hg and MMHg, estimated with the use of interfacial concentration gradients, constituted only a minor portion of the measured fluxes, suggesting the importance of advective processes on sediment-water exchange. Surface-water transect and time series studies conducted in Franks Tract support the commonly held belief that wetland and marsh regions are major sources for MMHg within the Delta. The integrated sediment-water fluxes of Hg and MMHg in the study area were estimated to be 130 and 6 mmol d Ϫ1 , respectively, and the benthic input was as important a source of Hg and MMHg as the riverine input within the Delta during low-flow months.