By using pollution source survey data, sewage treatment plant data, sediment monitoring results and SWMM, this study estimated the non-point source and overflow load of the basin. By analyzing the spatial and temporal distribution of major pollutants, the following results were obtained. 1) The chemical oxygen demand (COD), ammonia nitrogen (NH₃-N) and total phosphorous (TP) loads in Shenzhen River basin in 2015 were 36760 t/a, 5715.65 t/a and 494.36 t/a, respectively. The COD, NH₃-N and TP loads of the point source were 26300 t/a, 5496.9 t/a, and 463.55 t/a. The point source accounts for 72% of COD, 96% of NH₃-N, and 94% of TP of the whole year. The COD, NH₃-N and TP loads of the non-point source were 8608 t/a, 99.8 t/a and 18 t/a. The COD, NH₃-N and TP loads of the overflow in rainy season (April to September) were 1894.05 t, 118.95 t and 12.81 t. 2) The COD, NH₃-N and TP loads in Shenzhen Bay basin in 2015 were 116.5 t/d, 15.75 t/d and 1.412 t/d; the sewage outlets and the leakage sewage to tributary were the largest proportion of all source during the dry season. The COD, NH₃-N and TP loads of the point source were 71.94 t/d, 15.06 t/d, and 1.27 t/d during the dry season. During the rainy season, the non-point source COD accounted for the largest proportion (34.21%), followed by and the leakage sewage to tributary and the sewage outlets, which were 28.73% and 22.3%. 3) Due to a large amount of pollutant load were transported into the waterbody, the pollutant load from non-point source and overflow considerably effected the water quality during the rainy season that could not be ignored, especially in the rainy days, and it took a long time to return to normal water quality.