In recent years, the Miyun Reservoir faces severe problems of water quality and quantity due to continuous drought. In order to simulate and predict the eutrophic status of the Miyun Reservoir and its watershed, an integrated model was developed based on GIS and RS technology, which was composed of non-point source (NPS) simulation model, aquatic ecological-hydrodynamic model, and river water quality model. Ecological-hydrodynamic model was developed through coupling water quality analysis simulation program (WASP) with environmental fluid dynamics Code (EFDC). SWAT was selected as NPS simulation model, which could also perform water quality simulation in the river. Then the integrated model was calibrated using Markov Chain Monte Carlo method and verified using observed data. Results indicated that observed water quality data laid around the mode curves of simulation distribution, and which also dropped into the confidence interval on 80 percent credibility of water quality simulation distribution. In conclusion, the results show that the integrated model can meet the need of application.