In the coupled estuary–shelf system, plumes originating from the New Hu-Wei and Choshui rivers, consisting of many terrestrial materials, could contaminate the water of the Mailiao industrial harbor. To determine the contribution of the two rivers to pollution, the interaction between river-forced, tide-generating, and monsoon-driven water motions in and around the Mailiao industrial zone harbor was examined by performing a series of numerical model experiments. We used a three-dimensional general circulation model to examine the interplay between Asian monsoon-driven, river-forced, and tide-induced water motions, one of which could primarily affect the plume. The model-derived results for different river discharges revealed that almost all of the ammonium entering the harbor had a slope-positive trend, with oscillations in response to flood–ebb tidal cycles. The ammonium increased with time and flux, except for the 10 m3/s flux. Although the river discharge flux exceeded 200 m3/s, the ammonium entering the harbor was the same as that of the 200 m3/s flux; the ammonium concentration did not increase significantly with time after the flux exceeded 200 m3/s. In addition, irrespective of flood or ebb tidal currents being suppressed by strong Asian monsoons, this mechanism avoided contaminating the water quality of the harbor while northeasterly winds prevailed. By contrast, the southwesterly monsoon drove the geostrophic current northward along the coast; concurrently, the coastal sea level increased to form the surface isobar slope up toward the coast, producing a secondary flow to accelerate geostrophic alongshore currents. The northward geostrophic currents compressed the plumes shoreward, forming a relatively narrow-band plume; the coupling model demonstrated that the southwesterly monsoon-driven current pushed plumes favorably along the west pier into the harbor.