A three-dimensional hydrodynamic model was created to study the Danshuei River estuarine system and adjacent coastal ocean in Taiwan. The model was verified using measurements of the time-series water surface elevation, tidal current, and salinity from 1999. We conclude that our model is consistent with these observations. Our particle-tracking model was also used to explore the transport of particles released from the Hsin-Hai Bridge, an area that is heavily polluted. The results suggest that it takes a much longer time for the estuary to be flushed out under low freshwater discharge conditions than with high freshwater discharge. We conclude that the northeast and southwest winds minimally impact particle dispersion in the estuary. The particles fail to settle to the bottom in the absence of density-induced circulation. Our model was also used to simulate the ocean outfall at the Bali. Our experimental results suggest that the tidal current dominates the particle trajectories and influences the transport properties in the absence of a wind stress condition. The particles tend to move northeast or southwest along the coast when northeast or southwest winds prevail. Our data suggest that wind-driven currents and tidal currents play important roles in water movement as linked with ocean outfall in the context of the Danshuei River.