Spatial and temporal distributions of total and methyl mercury and controlling factors were investigated based on cold vapor atomic fluorescence detection. Total mercury levels in the whole sediments are (0.392 +/- 0.070) microg/g, without significant variations between different seasons, but generally increase toward the sediment-water interface. Total mercury levels are higher compared to data reported in other uncontaminated reservoirs and Wujiangdu Reservoir. This indicates there are mercury contaminations in Hongfeng Reservoir. Methyl mercury concentrations are highest in spring, without significant variations in other seasons. The peak values of methyl mercury typically appear in the upper 8 cm of the sediment profiles which are also the zones of sulfate-reducing bacteria activities. The seasonal variation and maximum peak value distributions of methyl mercury in sediment are mainly controlled by seasonally migration of oxic/anoxic boundary layer. Total mercury concentrations in the pore water and partition coefficients for THg in solid phase and water phase are mainly controlled by temperature or redox potential. Total mercury concentrations in the pore water have no relationship with total mercury concentrations in solid phase. However, the methyl mercury concentrations in the pore water have a strong relationship with those in solid phase (r = 0.70, p < 0.001). The methyl mercury concentrations in solid phase and pore water are controlled by solid/water partition coefficient, as well as methyl mercury production.