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A coupled model is an effective tool to understand the nutrient fate associated with hydrodynamic and ecosystem processes and thereby developing a water resource management strategy. This paper presents a coupled modeling approach that consists of a watershed model and a hydrodynamic model to evaluate the nutrient fate in a river-reservoir system. The results obtained from the model showed a good agreement with field observations. The results revealed that the Shuikou reservoir (Fuzhou, China)exhibited complicated hydrodynamic characteristics, which may induce the pattern of nutrient export. Reservoirs can greatly lower water quality as a result of decreasing water movement. Three scenarios were analyzed for water management. The NH3-N (Ammonia Nitrogen) decreased sharply in the outlet of Shuikou reservoir after NH3-N level in its tributary was reduced. After removing the farming cages, the water quality of the outlet of Shuikou reservoir was improved significantly. The DO (Dissolved Oxygen) had increased by 3%-10%, NH3-N had reduced by 5%-17%, and TP (Total Phosphorus) had reduced by 6%-21%. This study demonstrates that the proposed coupled modeling approach can effectively characterize waterway risks for water management in such a river-reservoir system.