Gunsan coastal area is one of region increasing pollution problems. To improve water quality, the reduction of these nutrients loads should be indispensible. In this study, the three-dimensional numerical hydrodynamic and ecosystem model were applied to analyze the processes affecting the eutrophication. In field survey, the average concentrations of dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus(DIP) at surface waters were found to be 0.43mg/$ell$ and 0.03mg/$ell$ respectively, which were exceeding second grade of water quality criteria. In hydrodynamic modelling, the comparison between the simulated and observed tidal ellipses showed fairly good agreement. The ecosystem model was calibrated with the observed data in study area. The simulated results of DIN were fairly good coincided with the observed values within relative error of 32.39%, correlation coefficient(r) of 0.99. In the case of DIP, the simulated results were fairly good coincided with the observed values within relative error of 24.26%, correlation coefficient(r) of 0.82. The simulations of DIN and DIP concentrations using ecosystem model were performed under the conditions of 20∼80% reductions for pollutant loading. At simulation results, concentration of DIN and DIP were reduced to 20∼80% and under 10% in case of the 80% reduction of pollutant loading, respectively.