Abstract: The Fenhe reservoir is the regulating reservoir of the Yellow River diversion project and the biggest surface drinking water sources project of Shanxi Province, and the COD (chemical oxygen demand) and TN (total nitrogen) in the upper reaches of the reservoir are beyond the standards. For ensuring the water quality safety of the reservoir, it’s crucial to determine the law of pollutants’ transport and diffusion and put forward relative protection measures. Based on the engineering data, the DEM model and the meseared information obtained from the remote sensing (RS) and global position system (GPS), the digital processing of the boundary and terrain for Fenhe reservoir by geographic information system (GIS) has been finished; using the measured data to calibrate parameters and verify the model, the hydrodynamic model and a water quality model for Fenhe reservoir have been developed; and on the basis of the hydrodynamics of Fenhe reservoir, we couple the two models, select the characteristic values of COD and TN to numerically simulate and calculate the reservoir’s area where the pollutants are over standards under different pollution concentrations during inflowing. The percentage of the area (Ae) where pollutants are over standards has been taken as a mark of the pollution degrees in the reservoir. It is found that the wind is the main factor influencing the reservoir’s hydrodynamics. Under no-wind conditions, the COD and TN spread along the terrain; under wind conditions, the pollutants spread to the bank along the wind direction. There exists a quadratic function relationship between the Ae and the pollution concentration of influent. The research results will provide an important support for the water quality management of the reservoir. Through the control of the water pollutant concentration, the improvement of the reservoir dynamics and the reduction of the endogenous will be favorable to solving the problems of the water quality in the Fenhe reservoir.