With seasonal wetting and drying, and high biological productivity, agricultural wetlands (rice paddies) may enhance the conversion of inorganic mercury (Hg(II)) to methylmercury (MeHg), the more toxic, organic form that biomagnifies through food webs. Yet, the net balance of MeHg sources and sinks in seasonal wetland environments is poorly understood because it requires an annual, integrated assessment across biota, sediment, and water components. We examined a suite of wetlands managed for rice crops or wildlife during 2007–2008 in California's Central Valley, in an area affected by Hg contamination from historic mining practices. Hydrologic management of agricultural wetlands for rice, wild rice, or fallowed — drying for field preparation and harvest, and flooding for crop growth and post-harvest rice straw decay — led to pronounced seasonality in sediment and aqueous MeHg concentrations that were up to 95-fold higher than those measured concurrently in adjacent, non-agricultural permanently-flooded and seasonally-flooded wetlands. Flooding promoted microbial MeHg production in surface sediment of all wetlands, but extended water residence time appeared to preferentially enhance MeHg degradation and storage. When incoming MeHg loads were elevated, individual fields often served as a MeHg sink, rather than a source. Slow, horizontal flow of shallow water in the agricultural wetlands led to increased importance of vertical hydrologic fluxes, including evapoconcentration of surface water MeHg and transpiration-driven advection into the root zone, promoting temporary soil storage of MeHg. Although this hydrology limited MeHg export from wetlands, it also increased MeHg exposure to resident fish via greater in situ aqueous MeHg concentrations. Our results suggest that the combined traits of agricultural wetlands — slow-moving shallow water, manipulated flooding and drying, abundant labile plant matter, and management for wildlife — may enhance microbial methylation of Hg(II) and MeHg exposure to local biota, as well as export to downstream habitats during uncontrolled winter-flow events.