With China’s rapid economic growth and increasing speed of urbanization, water pollution accidents have become one kind of environmental pollution source in China and bring potential risk to urban drinking water safety. The Huangjuedu Drinking Water Source Area is an important water source in Chongqing City (Southwest China) and a water intake source for the Jiangnan Waterworks of the Chongqing Drinking Water Company. There are still risks of water pollution accidents caused by ship leakage, road traffic accidents, chemical plant leakage, etc. The safety of the drinking water area is related to regional residents’ health and life safety and also has a profound impact on economy development and social stability. To reduce the harmful impacts of water pollution, it is of great scientific value and practical significance to analyze the pollutant diffusion of water pollution accidents with the Three Gorges Reservoir Area drinking water source security platform. In this paper, a two-dimensional water quality monitoring model was applied, and the digital elevation model was incorporated into the geographic information system, which generated a computational grid. Then, the Three Gorges Reservoir Area drinking water source security platform was developed. The platform can predict the water flow velocity, pollutant concentration at the drinking water inlet, and the spatial and temporal distribution of pollutants in the whole water source area. Furthermore, a hypothetical ammonia nitrogen leak accident was analyzed using this safety platform. The ammonia nitrogen concentration at the intake of the drinking water source area was detected and analyzed by the security platform from the time of the accident until the concentration dropped to the background during four water periods under different wind direction conditions. The pollutants took 19, 22, 25, and 40 min to reach the water quality standard during the four water periods. Moreover, the diffusion of ammonia nitrogen in the southeast wind was faster than that in the southwest wind. The results showed that the platform is scientific and practical, and the prediction results are helpful for the Emergency Management Department to quickly and accurately predict the migration of ammonia nitrogen pollution and make corresponding plans under accident conditions.