The distribution of mercury (Hg) in four different water bodies (streams, pond, precipitation and wells) of a small typical agricultural watershed in the Three Gorges Reservoir region was studied during the period from November 2011 to September 2012. Total mercury (THg) and methylmercury (TMeHg) concentrations ranged from 1.12 ng x L(-1) to 64.04 ng x L(-1) and from 0 (undetected) to 4.24 ng x L(-1), with an average of (13.54 ± 10.55) ng x L(-1) and (0.22 ± 0.42) ng x L(-1), respectively. Particulate mercury (PHg) accounted for a major fraction of THg in these four water bodies, whereas for TMeHg dissolved fraction dominated in wells and streams, but not in pond and precipitation. An obvious spatial pattern of Hg distribution was observed with THg concentration in the order of precipitation > pond > streams > wells and streams > pond > precipitation > wells for TMeHg. The THg temporal distribution showed that THg concentrations in cold season were higher than that in warm season, but the temporal distribution of TMeHg varied with the water types. Comprehensive data analysis found that wet deposition was a significant source of Hg in this agricultural watershed and the particulate transport was the main way for Hg and MeHg transport in this watershed. In addition, surface runoff was an important process for Hg contribution from watershed to the Three Gorges Reservoir, but played a minor role for TMeHg load to the reservoir.