The Three Gorges Reservoir area is recognized by its vast size, dense population, bustling economic and social activities along its banks, and by the significant volume of waterway traffic. These factors make it with a high risk of water pollution accidents, posing a serious threat to water environmental safety. Therefore, it is imperative to conduct a water environmental safety assessment in this region to ensure the safety of the water environment. In the present work, the Driving-Pressure-State-Impact-Response-Risk Water Environmental Safety model was proposed, and a comprehensive water environmental safety assessment system was established. The Water Environment Safety Index was introduced to measure the degree of water environment safety. This model synthesized multiple factors and their interrelationships, enabling a more accurate assessment of water environment safety. By adopting scientifically rigorous evaluation criteria, this assessment method enhanced the reliability and credibility of the results obtained. The water environment safety in the 22 counties and districts of the Three Gorges Reservoir area of Chongqing region from 2017 to 2021 was assessed in terms of temporal changes and spatial differentiation. In general, the overall water environment safety situation in the Three Gorges Reservoir area of Chongqing region is relatively safe, but a few counties/districts (such as Wanzhou District, Jiangjin District, etc.) are still in Warning. Spatially, the water environmental safety condition was relatively better in the northeast compared to the southwest. The main factors threatening water environment safety include: 1) the consequence of the Three Gorges Project, 2) severe soil erosion, 3) industrial, agricultural, and domestic pollution, and 4) frequent water pollution accidents. The present work provided a new method for conducting water environment safety assessments, which is expected to positively contribute to further research in this field.