Methylmercury (MeHg) is a toxic and bioaccumulative form of mercury that can be produced by bacteria living in water saturated soils, including those found in flooded rice fields. In the Sacramento Valley, California, rice is grown on 240,000 hectares, and mercury is a concern due to a history of mining in the surrounding mountains. Using unfiltered aqueous MeHg data from MeHg monitoring programs in the Sacramento River watershed from 1996 to 2007, the MeHg contribution from rice systems to the Sacramento River, was assessed. AgDrain MeHg concentrations were elevated compared to upstream river water during November through May, but were not significantly different during June through October. June through October AgDrain MeHg loads (concentration × flow) contributed 10.7–14.8% of the total Sacramento River MeHg load. Missing flow data prevented calculation of the percent contribution of AgDrains in November through May. Field scale MeHg dynamics were studied in two commercial rice fields in the Sacramento Valley. The Studied fields had soil total mercury concentrations of 25 and 57 ng g−1, which is near the global background level. Surface water and rice grain MeHg and THg concentrations were low compared to previously studied fields. An analysis of surface water drainage loads indicates that both fields were net MeHg importers during the growing season and net MeHg exporters during the fallow season. Since the microbes that produce MeHg prefer flooded environments, management that dries the soil might reduce MeHg production. Conventional continuously flooded (CF) rice field water management was compared to alternate wetting and drying, where irrigation was stopped twice during the growing season, allowing soil to dry to 35% volumetric moisture content, at which point plots were re-flooded (AWD-35). Compared to CF, AWD-35 resulted in a significant reduction of MeHg concentration in soil, surface water and rice grain.