[Objective] The distribution characteristics of water pollution risk in inland river basins were analyzed. A regional assessment was conducted to provide theoretical support and reference for the study of water pollution risks and incidents in inland river basins. [Methods] Geographic information system (GIS) spatial analysis was used to refine and visualize the degree and distribution of water pollution risk based on environmental statistical data, digital elevation model(DEM) data, water quality monitoring section data, and basic geographic data of the Heihe River basin in 2021, and a 1 km×1 km grid as the basic unit. The environmental risk field was used to assess the water pollution risk in the Heihe River basin and to analyze the distribution characteristics of water pollution risk zoning. [Results] Only a few areas in the Heihe River basin were at high-risk levels. Severly polluted water systems were mainly concentrated in the middle and lower reaches of the river, including Hongshui River, Taolai River system, and many rivers such as the Heidaban River from Shandan Ciyaokou to the Gaotai, main stream of Heihe River, and Liyuan River, Nineteen high-risk “hot spots” in the Heihe River basin have been accurately identified. Severe pollution was mainly distributed in the risk sources around the water system and in the overlapping areas of roads along the river, bridges across the river, and companion sections of the water system. The risk of water pollution in the entire Heihe River basin was low and within a manageable range. [Conclusion] This evaluation index system can characterize the main problems of water pollution risk in inland river basins from multi-dimensional and multi-spatial perspectives to improve the evaluation index system of water pollution risk in these basins and the level of risk management in the entire river basin.