In order to assist the water quality management in Miyun Reservoir, a spatial and dynamic simulation model system was built. In the model system, GIS was integrated with the WASP5 model. The integrated model system was then calibrated and verified in different sets of field data. The result showed that the integrated model system could characterize the Miyun Reservoir waters. Two scenarios were then designed and analyzed with the integrated model system. It was indicated that the water quality would improve if the cage fishery was banned, the algae blooms might occur in Miyun Reservoir if the low water stage ocurred but loads remained unchanged.