A three-dimensional, time-dependent, baroclinic, hydrodynamic and salinity model, UnTRIM, was performed and applied to the Danshuei River estuarine system and adjacent coastal sea in northern 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 wind stress and freshwater discharge on Dasnhuei River plume. As the absence of wind stress, the anticyclonic circulation is prevailed along the north to west coast. The model results reveal when winds are downwelling-favorable, the surface low-salinity waters are flushed out and move to southwest coast. Conversely, large amounts of low-salinity water flushed out the Danshuei River mouth during upwelling-favorable winds, as the buoyancy-driven circulation is reversed. Wind stress and freshwater discharge are shown to control the plume structure.