Water quality risk assessment is an important part of lake water quality management. A large number of water diversion project have been built around the world, which not only alleviate the problems of declining Lake water level and water scarcity, but also have complex impacts on lake water quality risk. This article took Lake Chaohu in China as a typical area, constructed a water quality model, and used scenario analysis method to evaluate the impact of the water diversion project (i.e. the Yangtze River to Huaihe River Water Diversion Project) on the water quality risk of Lake Chaohu. The results indicated that the water diversion project has a nonnegligible impact on the water quality risk of Lake Chaohu. Water diversion would alter the total nitrogen and total phosphorus concentrations of the lake. The difference between the water quality of water source and the background water quality of the lake would change the impact of the diversion project on lake water quality risk. Due to the higher total nitrogen in the water source compared to the lake, there was a risk of an increase in the total nitrogen in the lake after water diversion. The permanganate index concentration of the water source was lower than that of the lake, so the permanganate index concentration of the lake might decrease. The results help deepen our understanding of lake water quality risk and provide support for lake water quality management under the influence of water transfer project.