One of the most important factors that cause eutrophication is nutrient materials containing nitrogen and phosphorus which stem from excreation of terrestial sources and release from sediment. Therefore, to improve water quality, the reduction of these nutrients loads should be indispensible. At this study, the three-dimensional numerical hydrodynamic and ecosystem model, which was developed by Institute for Resources and Environment of Japan, were applied to analyze the processes affecting the eutrophication. The residual currents, which were obtained by integrating the simulated tidal currents over 1 tidal cycle, showed the presence of a typical counterclockwise eddies between Gyewha and Garyuk island. Density driven currents were generated westward at surface and eastward at the bottom in Saemankeum area where the fresh waters are flowing into, The ecosystem model was calibrated with the data surveyed in the field of the study area in annual average. The simulated results were fairly good coincided with the observed values within relative error of $30\%$. The simulations of DIN and DIP concentrations were performed using ecosystem model under the conditions of $40~100\%$ pollution load reductions from pollution sources. In study area, concentration of DIN and DIP were reduced to $59\%$ and $28\%$ in case of the $80\%$ reduction of the input loads from fresh water respectively. But pollution loads from sediment had hardly affected DIN and DIP concentration, The $95\%$ input load abatement is necessary to meet the DIN and DIP concentration of second grade of ocean water quality criteria.