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.