The Three Gorges Reservoir is the largest freshwater resource reservoir in China. The water environment security in the Three Gorges Reservoir area has a prominent position in the major national strategy for the protection of the Yangtze River. Based on the pressure–state–response (PSR) model, this study comprehensively considers the dangerousness of risk source, the sensitivity of risk receptors, and the acceptable level of regional environmental risk to construct the grading evaluation index system of water environment pollution risk. By using spatial statistical methods, including the variation coefficient method and cold–hot spot pattern analysis, the risk distribution of water environment pollution in the Chongqing section of the Three Gorges Reservoir area was comprehensively identified and evaluated by administrative units. The results showed that: (1) the number of risk sources was largest in Yunyang County and the number of risk receptors was largest in Wanzhou District. However, the distribution of high-risk pollution sources and high-sensitivity receptors was most intensive in the main urban area and surrounding areas of Chongqing, and the regional environmental risk acceptance level was the lowest. (2) The statistical results of risk source dangerousness and the risk receptor sensitivity index at the county level in the study area showed an aggregated distribution pattern, with hotspot areas concentrated in the main urban area of Chongqing and the surrounding area in the upper reaches of the reservoir area. Moreover, the acceptable level of risk in this area showed a cold spot area, while other regions basically showed a balanced distribution pattern without forming significant hot spot or cold spot areas. (3) The high-risk river section of water pollution in the reservoir area comprised five counties, including Jiulongpo District, Yubei District, Shapingba District, Yuzhong District and Nanan District; the middle-risk river section comprised six counties, including Changshou District, Beipei District, Jiangbei District, Dadukou District, Fuling District and Shizhu County; and the low-risk river sections were mainly distributed in the Jiangjin District in the upper reaches of the reservoir area and the middle and lower reaches of the northeast ecological area of Chongqing. Therefore, the acceptable levels of water pollution risk sources, receptors and regional environmental risks in the Chongqing section of the Three Gorges Reservoir area are unevenly distributed, showing an aggregated distribution pattern. The spatial distribution of water environment pollution risk is uneven, and the significant potential risk area is the functional core area of Chongqing, which is the critical area of water environment risk management in the future.