A 3-D, time-dependent, baroclinic, hydrodynamic and salinity model was implemented and applied to the Danshuei River estuarine system and the adjacent coastal sea in Taiwan. The model forcing functions consist of tidal elevations along the open boundaries and freshwater inflows from the main stream and major tributaries in the Danshuei River estuarine system. The bottom friction coefficient was adjusted to achieve model calibration and verification in model simulations of barotropic and baroclinic flows. The turbulent diffusivities were ascertained through comparison of simulated salinity time series with observations. The model simulation results are in qualitative agreement with the available field data. The validated model was then used to investigate the influence of freshwater discharge on residual current and salinity intrusion under different freshwater inflow condition in the Danshuei River estuarine system. The model results reveal that the characteristic two-layered estuarine circulation prevails most of the time at Kuan-Du station near the river mouth. Comparing the estuarine circulation under low- and mean flow conditions, the circulation strengthens during low-flow period and its strength decreases at moderate river discharge. The river discharge is a dominating factor affecting the salinity intrusion in the estuarine system. A correlation between the distance of salt intrusion and freshwater discharge has been established allowing prediction of salt intrusion for different inflow conditions. ?? 2007 Elsevier Ltd. All rights reserved.