In this study, the material cycle model was applied to suggest alternative management of water quality for Jeju Harbor. The distribution of COD, DIN (dissolved inorganic nitrogen) and DIP (dissolved inorganic phosphorus) concentrations was reasonably reproduced by simulations on the model area of the Jeju Harbor using a material cycle model. The simulations of COD, DIN and DIP concentrations were performed under the conditions of 20∼100% pollution loadings reductions from pollution sources. In case of the 100% reduction of the input loads from Sanzi river, concentrations of COD, DM and DIP were reduced to 39%, 78% and 52%, respectively at Jeju harbor. In contrast, in case of the pollutant loadings reductions from sediment, the effect of DIN and DIP reduction relatively seemed to increase around the center of study area. The 95% reduction of the pollutant loadings from river and sediment is required to meet the COD and nutrients concentration of second grade of ocean water quality criteria.