The water levels of lakes along the eastern route of the South-to-North Water Diversion Project (ER-SNWDP) are expected to rise significantly and subsequently affect the process of flood control and drainage in those lake basins. However, few studies have focused on the impacts of interbasin water diversion on the flood control and drainage of water-receiving areas at the lake basin scale. Using MIKE software, this paper builds a coupled hydrodynamic model to address the existing literature gap on the impacts of interbasin water diversion on the process of flood control and drainage in a water-receiving lake basin, and it considers the many types of hydraulic structures in the model. First, a flood and waterlogging simulation model was constructed to simulate the interactions among the transferred water, waterlogging of the lakeside area surrounding Nansi Lake (NL), and water in NL and its tributaries. The ER-SNWDP was also considered in the model. Second, the model was calibrated and verified with measured data, and the results showed that the model is efficient and presents a Nash-Sutcliffe efficiency coefficient (NSE) between 0.65 and 0.99. Third, the process of flood and drainage in the lakeside area of NL was simulated under different water diversion and precipitation values. Finally, the impacts of emergency operations of the ER-SNWDP on flood control and waterlogging drainage in the lakeside area of NL were analyzed based on the results from the proposed model, and selected implications are presented for the integrated management of the interbasin water diversion and the affected lakes.