Water contamination in certain rivers during rainfall necessitates the evaluation of pollutant levels within pipelines and the identification of their sources to ensure effective pollution control. In this study, we assess pollutant concentrations during runoff from surfaces, pipelines, and channels, identify pollutant sources within pipelines, and analyze sewage leakage contributions to channel pollution in residential areas in Wuxi City, China. The results showed that the event mean concentrations of total nitrogen (TN), total phosphorus (TP), ammonium (NH4+-N), and nitrate (NO3--N) in the drainage outlet runoff were 3.4, 1.1, 8.8, and 14.9 times higher than in impervious surface runoff. The predominant forms of nitrogen and phosphorus in runoff shift from organic to inorganic as they move from the surface to pipelines. The pipeline load and contribution were further estimated by combining water quantity calculations from the calibrated and verified Storm Water Management Model (SWMM) with measured nitrogen and phosphorus concentrations in the runoff. TN, NH4+-N, NO3--N, and PO43--P within the pipelines accounted for 59%, 83%, 90%, and 77% of the discharge loads, respectively. The application of the Stable Isotope Analysis in R (SIAR) package (MixSIAR) revealed that the domestic sewage and soil organic N were the predominant sources of pollutants within drainage pipelines, contributing 23.7% and 32.6% of NO3--N, respectively. Additionally, the sewage leakage accounted for 33.7% and 66.9% of NO3--N in drainage runoff and channels, respectively. Unlike existing methods, this study quantitatively highlights the significant impact of pipeline pollutants and sewage leakage on urban river water quality, providing essential insights for developing effective strategies to mitigate non-point source water pollution.