According to small environmental capacity and fragile ecosystem of lake, the lakes in Chongqing Section of Three Gorges Reservoir Region were taken as a case. The effects of cold water discharge of lake water source heat pump systems on lake algae and Chla were studied with the method of physical simulation. It was found that cold discharge discouraged the growth of algae, and the critical temperature of algae growth was between 4.5℃ and 6.2℃. There was significant impact of cold discharge on dominant populations and its proportional change of algae. And it would reduce the number of algal populations and the content of Chla. Furthermore, the cold discharge would have great influence on total quantity of phytoplankton. And the higher the content of nitrogen and phosphorus of raw water was, the greater of the effect extent was.