The water environment of plain river networks can be self-cleaning to a certain extent, but if the wastewater load exceeds a certain threshold, it can disturb the natural balance and cause water pollution. This underlines the importance of water pollution control measures. However, the development of water pollution control measures requires a large number of hydrological and hydrodynamic parameters and the establishment of corresponding relationships through modelling. Therefore, this study mainly used the Infoworks ICM model to construct a detailed hydrological–hydrodynamic water environment analysis model for the Yundong area of Baoying County, Yangzhou City, China, screened the main pollution source areas and pollution time periods of the typical rivers in the study area, and proposed effective improvement measures according to the actual situation of the study area. The results show that after the synergistic effect of multiple measures, the water quality can reach the Class III standard (GB3838-2002). This study can provide a reference for the water environment management and improvement of the plain river network and has good application prospects.