With the development of cities, urban area source pollution has become more severe and a significant source of water pollution. To study the relationship between urban area source pollution and water environmental quality in a river network, this study uses a city in the Yangtze River Delta, China, as an example. The Storm Water Management Model (SWMM) model and the MIKE11 model were combined into a unified modeling framework and used to simulate dynamic changes in the water quality of a river network under light rain, moderate rain, and heavy rain. In the study period, the annual urban area source input loads of potassium permanganate (CODMn), total phosphorus (TP), and ammonia nitrogen were 29.8, 0.9, and 4.8 t, respectively. The influence of light rain on the water quality of the river network was lagging and temporary, and rainfall area pollution was the primary contributor. Under the scenario of moderate rain, overflow from a pipeline network compounded rainfall runoff, resulting in a longer duration of impact on the water quality in the river. Additionally, the water quality in the river course was worse under moderate rain than under light or heavy rain. Under the scenario of heavy rain, rain mainly served a dilutive function. This research can provide support for urban area source pollution control and management.