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According to small environmental capacity and fragile ecosystem of lake, take for the research object of lakes in Chongqing Section of three gorges reservoir area. Using the method of physical simulation, studied the effects of cold water discharge of lake water source heat pump systems on water quality. The results showed that cold water discharge lead to the water temperature decrease in local area of lake, thus, the Dissolved Oxygen near outfall week increased, but the bottom Dissolved Oxygen was unchanged; It also made the Alkalinity increasing to some degree, but the effect is not significant on pH; Cold discharge lead to increase of ammonia nitrogen, but had little effect on nitrate nitrogen; cold discharge had certain limit function on total nitrogen increasing, which was mainly the content of organic nitrogen reduce; The total Phosphorus also increase because of cold discharge, but it was not significant. The correlation between total nitrogen and total phosphorus was not remarkable.