The change of nonpoint source and freshwater discharge as a result of land use change might affect the water quality in a river. In the current study, a coupled three-dimensional hydrodynamic and water quality model was created and applied to the Danshuei River estuarine system and its adjacent coastal ocean. The hydrodynamic and water quality models were validated using observations of water surface elevation, salinity distribution and water quality state variables. The predictions of hydrodynamics, salinity, dissolved oxygen and nutrients from the model simulation quantitatively agreed with the observational data. The validated model was then used to investigate the possible effects of the nonpoint source and freshwater discharge changes at the upstream reaches on water quality conditions in the Danshuei River estuarine system. Three scenarios were investigated to predict the dissolved oxygen using model simulations. The simulated results indicated that increasing nonpoint sources at the upstream reaches degraded the dissolved oxygen under low flow conditions. However, increasing freshwater discharges at the upstream reaches would overcome the loadings of the nonpoint source, which would result in increasing the dissolved oxygen in the tidal river estuary. The model can provide a useful tool for developing management practices for nonpoint sources to protect the water quality in the estuarine system.
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