Methylmercury (MeHg) is a human and environmental toxin produced in flooded soils. Little is known about MeHg in rice (Oryza Sativa L.) fields in Sacramento Valley, California. The objectives of this study were to quantify mercury fractions in irrigation water and within rice fields and to determine their mercury pools in surface water, soil, and grain. Soil, grain, and surface water (dissolved and particulate) MeHg and total mercury (THg) were monitored in six commercial rice fields throughout a winter fallow season and subsequent growing season. Both dissolved and particulate mercury fractions were higher in fallow season rice field water. Total suspended solids and particulate mercury concentrations were positively correlated (r = 0.99 and 0.98 for THg and MeHg, respectively), suggesting that soil MeHg was suspended in the water column and potentially exported. Dissolved THg and MeHg concentrations were positively correlated with absorbance at 254 nm (r = 0.47 and 0.58, respectively) in fallow season field water. In the growing season, fields with higher irrigation water MeHg concentrations (due to recycled water use) had elevated field-water MeHg (r = 0.86) and grain MeHg concentrations (r = 0.96). Based on a mass balance analysis, soil mercury pools were orders of magnitude larger than surface water or grain mercury pools; however, fallow season drainage and grain harvest were the primary pathways for MeHg export. Based on these findings, reducing (1) discharge when water is turbid, (2) straw inputs, and (3) use of recycled irrigation water could help reduce mercury exports in rice field drainage water.