To estimate the impact of mercury released from an artisanal small-scale gold mining (ASGM) activities on the ecosystem. Total and organic mercury concentrations in paddy field soil and freshwater snails around an artisanal small-scale gold mining area were investigated. Paddy field soil samples and freshwater snails were collected from ten sites along the Cikaniki River. A site located in a national park, which was approximately 12 km upstream from the ASGM site, was considered the reference site for this study. The organic mercury concentration in soil samples collected at the ASGM site was n.d.–0.018 mg kg−1 and that at the reference site was 0.005–0.008 mg kg−1. The organic mercury concentrations in the freshwater snails collected at the ASGM and reference sites were 0.38 ± 0.21 mg kg−1 (31.0 ± 26.6% of total mercury, n = 38) and 0.056 ± 0.032 mg kg−1 (40.5 ± 11.5% of total mercury, n = 16), respectively. Although the original form of mercury in the mining waste was elemental mercury and/or Hg2+, the mercury form changed to organic mercury in environment and the organic mercury was concentrated two orders of magnitude, even in low-order organisms.