Estuaries, the confluence zones between river and sea, show a complex dynamic behavior. Saltwater intrusion can lead to a more or less well-defined salt wedge with associated with density current. The main factors that affect the flow conditions in an estuarine system are tides, varying of freshwater discharge with seasonal variation, and intrusion of saltwater from the ocean. The computed tidal ranges and time series salinity using the three-dimensional hydrodynamic and salinity model compare with observed data. The comparison results show that they are in good agreement. The validated model was then adopted to investigate the effects of different freshwater discharges on saltwater intrusion and circulation in the Danshuei River estuarine system. It shows that the distance of saltwater intrusion under low freshwater discharge (Q75 flow) is longer than that under mean freshwater discharge. Observed distances of saltwater intrusion match the simulated results. The relationships between the distance of saltwater intrusion and freshwater discharge were also established through the model prediction.