In order to research the impact of continuous extreme rainfall on the water quality of the Dongjiang River, which is a drinking water source, the characteristics of extreme rainfall events in the basin were analyzed for last 38 years. The impacts of these events on water quality are discussed by considering both hydrological data and water quality data. Using SWAT2012 software, a high-precision basin model was established for the flux of major pollutants during extreme rainfall and water quality. The results indicate that there were 173 extreme rainfall events in the Dongjiang River basin over the past 38 years. The annual frequency of extreme rainfall events in high-flow years was higher than in other years. During the year, rainfall was mainly affected by climate, particularly from March to September (80%), with the peak rainfall usually occurring in June. Spatially, the Zengcheng-Bolo-Huizhou-Longmen area had the highest frequency of extreme events. During the study period, rainfall was significantly positively correlated with the concentrations of cyanide, Pb, Fe, Mn, TP, and with turbidity, and the correlation coefficients for the concentrations of TP and turbidity with rainfall were relatively high. Rainfall was significantly negatively correlated with pH, conductivity, the concentration of Zn, as well as some other indicators. These observations show that water quality is affected by rainfall to some extent. Turbidity, TN, ammonia nitrogen, and TP concentrations all showed increasing trends, to different degrees, during rainstorm runoff periods. Turbidity and TP concentrations showed a significant and consistent relationship with flow rate, peaking earlier than the flow rate peak (by approximately 1 d), showing a significant initial flushing effect. The pH curve showed an opposite trend to the flow rate, forming a "V" shape, which may be affected by the rainfall, soil acidity, and confluence conditions in the upstream mountains. Ammonia nitrogen was subject to initial flushing in the early stages of extreme rainfall but was diluted by the clean rainwater; initially, ammonia nitrogen showed high values that declined during the middle and late stages. The variations in pollutant loads were consistent with that of runoff flux, and the peaks in TN, ammonia nitrogen, and TP flux appeared later than the flow peak (by approximately 1 d), thus differing from the pollutant concentration peak. The pollutant load mainly showed a significant increase during storm runoff periods. The proportion of pollutant COD, ammonia nitrogen, and TP transported by 59.48% of the runoff reached 68.42%, 54.68%, and 70.20%, respectively, demonstrating the characteristics of rapid and high-impact pollutant loads. These characteristics have a great influence on the quality of Dongjiang River drinking water and it is suggested that initial rainwater treatment should be strengthened to reduce the negative impact of rainstorm runoff periods on water quality.