With the effective control of point source pollution, non-point source and sewer overflow pollution becomes the main type of water pollution. Based on materials of land use, urban drainage network and so on, the basin-bay integrated water environmental model was established, and the spatio-temporal characteristics of non-point source and sewer overflow pollution in Shenzhen Bay Basin as well as its impacts on water environment were analyzed. Results showed that (1) The non-point source and sewer overflow pollution loading per unit area of COD, NH₃-N and TP in rainy season was 17.21 t/km²and 10.21 t/km², 0.17 t/km²and 0.69 t/km², 0.04 t/km² and 0.07 t/km², respectively; (2) The non-point source and sewer overflow pollution was concentrated in May and August with more heavy rainfall observed in Shenzhen River Basin, Dasha River Basin and Xinzhou River Basin with larger area, steeper surface slope and more sewerage cutting projects; (3) The COD, NH₃-N and TP concentrations of non-point source and sewer overflow pollution could approach 3.7, 18.2 and 8.5 times the values of water quality standards, respectively; (4) The areas where the COD, NH₃-N and TP concentrations in rainy season were higher than those in dry season exceeded 40%, 60% and 65% of the total area of Shenzhen Bay, respectively.