There are many watercraft and production accidents in the Three Gorges Reservoir Area (TGRA) of the Yangtze River in China every year. Accidents threaten the water quality of the 1085 km2 surface area of the TGRA and millions of local people if oil andchemical leakage were to occur. A water pollution management system for emergency response (WPMS_ER) was therefore designed for the management of pollution in this area. An integrated geographic information system (GIS)-based water pollution management information system for the TGRA, called WPMS_ER_TGRA, was developed in this study. ArcGIS engine was used as the system development platform, and Visual Basic as the programming language. The models for hydraulic and water quality simulation and the generation of body-fitted coordinates were developed and programmed as a dynamically linked library file using Visual Basic, and they can be launched by other computer programs. Subsequently, the GIS-based information system was applied to the emergency water pollution management of a shipwreck releasing 10 tons of phenol into the Yangtze River during two hours. The results showed that WPMS_ER_TGRA can assist with emergency water pollution management and simulate the transfer and diffusion of accidental pollutants in the river. Furthermore, it can quickly identify the affected area and how it will change over time within a few minutes of an accident occurring.