To analyse the influence of nonpoint source pollution on the water quality in the Daheiting Reservoir, based on measured hydrological and water quality data, a coupled hydrological model for the Panjiakou-Daheiting interval basin and a two-dimensional vertical hydrodynamic and water quality model for the Daheiting Reservoir were constructed. The water quantity and water quality output results of the upstream hydrological model (Soil and Water Assessment Tool, SWAT) were input into the reservoir hydrodynamic-water quality model (CE-QUAL-W2) as boundary conditions. The annual distribution of pollutants in the reservoir was simulated and analysed. The results showed that nutrients such as nitrate nitrogen and phosphate in the reservoir area were stratified, and there were seasonal differences due to the water temperature, dissolved oxygen and upstream inflow. After lowering upstream pollution emissions, the water quality in the reservoir was improved significantly, and compared to that of reducing point source pollution, the effect of reducing nonpoint source pollution is more obvious.