Rice paddy soil, as a typical ephemeral wetland, is known to be a significant environment for mercury (Hg) methylation. The methylation of inorganic mercury (IHg) in rice paddy soil constitutes a key step in the cycling of Hg in this special terrestrial ecosystem. An understanding of the factors that control the methylmercury (MeHg) production is necessary to underpin more reliable risk assessment and appropriate strategies to remediate contaminated soil. In this study, we compared the source and distribution of Hg species in different compartments of the rice paddy during a complete rice growing season at two different typical Hg-contaminated mining sites in Guizhou province, China: an abandoned site and a current-day artisanal site. In-situ specific methylation/demethylation rate constants in rice paddy soil were qualified using stable Hg isotope addition technique, simultaneously. The possible biogeochemical controls on MeHg production within the rice paddy ecosystem were further discussed in current study. Results showed that the dominant source of MeHg to paddy soil is in situ methylation of IHg. MeHg levels in rice paddy soil were a function of both methylation/demethylation processes and the net methylation potential in the rice paddy soil reflected the measured MeHg. Sulfate stimulating the activity of sulfate-reducing bacteria was a potentially important metabolic pathway for Hg methylation in rice paddies. Bioavailable Hg derived from new atmospheric deposition appears to be the primary factor regulating net MeHg production in rice paddies. We propose that the concentration of Hg in ambient air is an indicator for the risk of MeHg accumulation in paddy rice.