Forested catchments are an important part of the mercury (Hg) cycle and a link between the atmospheric and the aquatic environments. In this study, Hg input and output fluxes and its retention were investigated at subtropical forested catchments in southwest China. Significantly enhanced atmospheric Hg inputs were observed, and the contribution of litterfall Hg plays a more important role at these subtropical forested catchments. The ratios of Hg output fluxes from stream water to total input were 2.5% and 1.2% for LGS and TSP, which were markedly lower than those reported from Europe and North America. The current annual input Hg only accounted for 0.8 and 1.8 per mille to the Hg stored in the upper 90 cm of soil in LGS and TSP. These suggest that subtropical forested catchments are important for retention of atmospheric mercury deposition in southwest China.