The seasonal and spatial variability of water quality, including mercury species, was evaluated in agricultural and managed, non-agricultural wetlands in the Yolo Bypass Wildlife Area, an area managed for multiple beneficial uses including bird habitat and rice farming. The study was conducted during an 11-month period (June 2007 to April 2008) that included a summer growing season and flooded conditions during winter. Methylmercury (MeHg) concentrations in surface water varied over a wide range (0.1 to 37 ng L−1 unfiltered; 0.04 to 7.3 ng L−1 filtered). Maximum MeHg values are among the highest ever recorded in wetlands. Highest MeHg concentrations in unfiltered surface water were observed in drainage from wild rice fields during harvest (September 2007), and in white rice fields with decomposing rice straw during regional flooding (February 2008). The ratio of MeHg to total mercury (MeHg/THg) increased about 20-fold in both unfiltered and filtered water during the growing season (June to August 2007) in the white and wild rice fields, and about 5-fold in fallow fields (July to August 2007), while there was little to no change in MeHg/THg in the permanent wetland. Sulfate-bearing fertilizer had no effect on Hg(II) methylation, as sulfate-reducing bacteria were not sulfate limited in these agricultural wetlands. Concentrations of MeHg in filtered and unfiltered water correlated with filtered Fe, filtered Mn, DOC, and two indicators of sulfate reduction: the SO4 2 −/Cl− ratio, and δ34S in aqueous sulfate. These relationships suggest that microbial reduction of SO4 2−, Fe(III), and possibly Mn(IV) may contribute to net Hg(II)-methylation in this setting.