Water transfer projects in China have become a popular research topic in recent years. This study develops a method for evaluating the comprehensive impacts of water transfer projects on regional development. In the qualitative assessment, the comprehensive index method is employed, and an evaluation index system is established from economic, social and environmental perspectives. In this approach, the weights are determined by the analytic hierarchy process (AHP) and the entropy combined method. In the quantitative assessment, the sharing coefficient method is used. The procedure is applied to the water transfer project from the Yangtze River to the Taihu Lake. The qualitative results indicate that the conclusion of the water transfer project had a ‘large positive impact’ in 2016. In the quantitative assessment, the comprehensive benefit of increasing water supply via the project was 1.87 billion CNY in 2016. In addition, the integrated impact assessment method can be implemented at the seasonal scale to produce refined results. These results show that the proposed method can provide technical support for project operation and policy formulation.