The frequent occurrence of sudden water pollution accidents in the Dongjiang River basin poses severe challenges to the human health and ecological security of the regional population. Environmental Risk Zoning is a fundamental and effective tool for environmental risk management. Based on the Annual Environmental Statistics Yearbook, DEM, National Water Quality Monitoring Data and basic geographical data, and by adopting the spatial analysis method of Geographic Information System and Regional Growth Method, the paper zoned and classified the risk of water environment at a grid map of Dongjiang River basin with the resolution of 1 km×1 km. The results show that (1) the high-risk area is 696.7 km², accounting for 1.99% of the total assessed area. The relatively high-risk area is 1458.4 km², accounting for 4.17%. The middle-risk area is 2762.0 km², accounting for 7.90%. The low-risk area is 30031.7 km², accounting for 85.93%. (2) According to average risk value, the Shima river basin has the highest risk, followed by Tamsui river basin and Gongzhuang river basin. (3) From the mainstream distributional perspective, the area of high risk areas increases gradually from the upstream to the downstream of the Dongjiang River, mainly distributed in Longchuan county, Boluo county, Dongguan city, Shenzhen and other places. From the tributaries distributional perspective, the high risk areas are mainly distributed in Huizhou, Shenzhen and other places. The research results can provide theoretical and technical support for ecological and environmental management of Dongjiang River basin.