Understanding mercury (Hg) methylation/demethylation processes and the factors controlling methyl mercury (MeHg) production within the rice paddy ecosystem of Hg mining areas is critical to assess the risk of MeHg contamination in rice grain. Two typical Hg-contaminated mining sites, a current-day artisanal site (Gouxi) and an abandoned site (Wukeng), were chosen in this study. We qualified the in situ specific methylation/demethylation rate constants in rice paddy soil during a complete rice-growing season. Our results demonstrate that MeHg levels in rice paddy soil were a function of both methylation and demethylation processes and the net methylation potential in the rice paddy soil reflected the measured MeHg production at any time point. Sulfate stimulating the activity of sulfate-reducing bacteria was a potentially important metabolic pathway for Hg methylation in rice paddies. We suggest that bioavailable Hg derived from new atmospheric deposition appears to be the primary factor regulating net MeHg production in rice paddies.