This study aimed to assess the impact of livestock excreta discharged from an Intensive Livestock Farming Area (ILFA) on river water quality during a rainfall event. The Bangcho River, which is one of the 7 tributaries in the Cheongmi River watershed, was the study site. The Cheongmi River watershed is the second largest area for livestock excreta discharge in Korea. Our results clearly showed that, during the rainfall event, the water quality of the Bangcho River was severely deteriorated due to the COD, NH4-N, T-N, PO4-P, T-P, and heavy metals (Cu, Zn, and Mn) in the run-off from nearby farmlands, where the soil comprised composted manure and unmanaged livestock excreta. In addition, stable isotope analysis revealed that most of nitrogen (NH4-N and NO3-N) in the run-off was from the ammonium and nitrate in the livestock excreta. The values of δ15NNH4 and δ15NNO3 for the Bangcho River water sample, which was obtained from the downstream of mixing zone for run-off water, were lower than those for the run-off water. This indicates that there were other nitrogen sources upstream river in the river. It was assumed from δ15NNH4 and δ15NNO3 stable isotope analyses that these other nitrogen sources were naturally occurring soil nitrogen, nitrogen from chemical fertilizers, sewage, and livestock excreta. Therefore, the use of physicochemical characteristics and nitrogen stable isotopes in the water quality impact assessment enabled more effective analysis of nitrogen pollution from an ILFA during rainfall events.