Knowledge gaps of mercury (Hg) biogeochemical processes in the tropical rainforest limit our understanding of the global Hg mass budget. In this study, we applied Hg stable isotope tracing techniques to quantitatively understand the Hg fate and transport during the waterflows in a tropical rainforest including open-field precipitation, throughfall, and runoff. Hg concentrations in throughfall are 1.5−2 times of the levels in open-field rainfall. However, Hg deposition contributed by throughfall and open-field rainfall is comparable due to the water interception by vegetative biomasses. Runoff from the forest shows nearly one order of magnitude lower Hg concentration than those in throughfall. In contrast to the positive Δ 199 Hg and Δ 200 Hg signatures in openfield rainfall, throughfall water exhibits nearly zero signals of Δ 199 Hg and Δ 200 Hg, while runoff shows negative Δ 199 Hg and Δ 200 Hg signals. Using a binary mixing model, Hg in throughfall and runoff is primarily derived from atmospheric Hg 0 inputs, with average contributions of 65 ± 18 and 91 ± 6%, respectively. The combination of flux and isotopic modeling suggests that two-thirds of atmospheric Hg 2+ input is intercepted by vegetative biomass, with the remaining atmospheric Hg 2+ input captured by the forest floor. Overall, these findings shed light on simulation of Hg cycle in tropical forests.