Abstract: There are numerous pumping stations in the middle and lower reaches of Yangtze River, which are main channels for urban rainwater and sewage to the River. Jiangnan pumping station in the Great Tangxun Lake basin in Wuhan was taken as an example in this study. A two-dimensional hydrodynamic water quality model of the river section based on MIKE21 was built. The migration and diffusion characteristics of COD, NH₃-N, TP in the river section was simulated under three conditions, including normal discharge of sewage treatment plant tail water (ND), accident discharge of sewage treatment plant tail water (AD), and waterlogging drainage (WD). Compared with ND, the influence range and degree of WD on the concentration of water quality index in river reach increased significantly. The length and width of TP pollution zone exceeding Class II water quality standard increased by 2.66 times and 0.64 times, respectively. In addition, the TP concentration of the downstream Yangsigang national control section exceeded the standard by 0.16 times, which was equivalent to the impact of AD. Pumping station drainage was becoming a potential risk source of water quality exceeding the standard in flood seasons. The impact of pumping station drainage on the water environment was mainly controlled by the quality and flow of drainage. Developing a multi-objective operation and scheduling plan for pumping stations based on flood control safety, water environment protection, and other objectives was proposed for future research. It was suggested drainage pumping station in supervision and management of the river discharge outlet be considered, to force the improvement of water environment quality of cities along the River and to effectively reduce environmental risks of the main stream.