A three-dimensional eutrophication model was applied to assist the management of Dahuofang Reservoir in China. Transport processes were obtained from the three-dimensional, finite volume hydrodynamic model. The hydrodynamic model was verified for a one-year time period in 2006. Our simulation reproduced intra-annual variation of stratification. The simulated variation of vertical thermal structures also matched observations. The water quality model included 8 state variables, including dissolved oxygen, phytoplankton as carbon, carbonaceous biochemical oxygen demand, ammonium nitrogen, nitrate and nitrite nitrogen, ortho-phosphorus, organic nitrogen, and organic phosphorus. Sensitivity of the parameters has been analyzed to decide which process would affect the water quality in the simulation. The water quality verification suggested the model successfully computed the temporal cycles and spatial distributions of key water quality components. The comparison between water quality components before and after the first phase of the water conveyance project suggests that the project has a slight effect on the reservoir ecosystem. The model could be used as a tool to guide physico-biological engineering design or management strategies for Dahuofang Reservoir.Dahuofang Reservoir, reservoir, water quality, hydrodynamic, three-dimensional model PACS: 92.40.qf, 92.40.qc, 92.40.Cy, 92.40.We, 47.85.Dh