The geochemical processes of mercury in Dongfeng (DF) and Wujiangdu (WJD) reservoirs, which were constructed in 1992 and 1979, respectively in Wujiang River, which is the upper branch of Yangtze River were investigated. One sampling site was chosen up river of 1 km from the dam for each reservoir. Three sampling campaigns were conducted at these sampling sites in December 2003, April 2004 and July 2004, respectively. The distributions of different mercury species in the water column, sediment, and sediment pore water were studied. We found that the sediment is the net source of both inorganic and MeHg to the water column for both reservoirs. The MeHg diffusion fluxes in WJD reservoir at all sampling campaigns were significantly higher than those in DF reservoir. Our study demonstrated that the high primary productivity in the reservoir produced elevated organic matter content that would favor the methylmercury production in sediment.