The Three Gorges Project is built to sustainably exploit the water resource of the Three Gorges Valley. Water pollution prevention is imperious. Analyzing the mercury pollution situation of the Three Gorges Reservoir area in Chongqing territory reveals that the point sources of mercury pollution are mainly the urban point sources from drainage and industrial waste in Chongqing and Chang-shou and the non-point sources are mainly from severe erosion of the mercury-rich lands in the lower reaches of the Wujiang River resulting in large amount of mercury-rich soil runoff into rivers. It is suggested that sloping fields in the Reservoir Region be forested waste treatment facilities be updated plants discharging excessive mercury be shut, contaminated sediment and waste be moved into containments at safe locations and mercury pollutants be prevented from turning into the post poisonous methylmercury. In addition the water quality monitoring system should be updated and completed to identify and fix up problems in time an effective administrative mechanism should be established and environmental legislation should be reinforced to guarantee the well-ordered operation of the giant hydraulic works. Pro-environment practices to control the mercury pollution in Chongqing territory which is at the upper end of the Reservoir are essential to the safety of the Reservoir’s water resources.