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.　©　2019　by　the　authors.　Licensee　MDPI,　Basel,　Switzerland.