Spatiotemporal modeling of wetland environments’ hydrodynamics and water quality characteristics is key to understanding and managing these ecologically important areas’ physical and environmental properties. We developed a two-dimensional numerical model based on the MIKE 21 module to analyze flow and pollution dynamics in the island-dominated Sanyang wetland of eastern China. Three simulation periods representing annual precipitation cycles were used to model freshwater discharge and water quality in the wetland. The results showed that the flow velocity in the study area had hydrodynamic characteristics typical of such a setting, with an average monthly flow velocity ranging from 0.01 to 0.04 m/s, contributing to an increased risk of serious eutrophication. The water quality problems (represented by ammonia nitrogen, NH3-N, and total phosphorus, TP, levels) peaked during the early summer peak rain season, followed by a gradual decline during a later flood period and the lowest values during the fall/winter dry period. Moreover, the spatial distribution of NH3-N and TP levels decreased from northwest to east, reflecting the influence of a highly polluted source. Our results provide a useful context for restoration efforts in the Sanyang wetland and other similar areas.