The impacts of high water level running of three gorges dam on the reservoir water environment has always been a concerned problem. Taking Xiangxi River upstream of three gorges reservoir area as an example, the hydrodynamic and water quality of Xiangxi River would be simulated in this paper based on the mathematical model of Delft3D. First, the flow module was used to construct the hydrodynamic model in the study area, and the spatialtemporal hydrodynamic characteristics in flood season and storage period of 2013 were simulated. Second, the water quality model was built by using Waq module and NH+4 distribution was simulated after discharge of a large number of its emission. The modeling results showed that Xiangxi River in flood season was in a typical state of “River phase”, with a high flow rate. In the water storage period of the Three Gorges Reservoir, Xiangxi River is in a state like “lake phase”, the flow rate became very low and vortex was shaped. During the water storage period of the reservoir, the water level increased which caused slow river flow rate, and the hydrodynamic characteristics of Xiangxi River played a decisive role in the pollutant distribution. The water pollution characteristics of pollutants showed obvious flow back characteristics, which threatened Xiangxi river water quality. The study results can help provide support information for the management of the tributaries of the Three Gorges Reservoir area.