This study carried out current status, characteristics, and problems of coastal environment management on semi-enclosed Masan Bay in Korea and suggests cost-effective and eco-friendly water quality management policy. The pollutants from terrestrial sources into the Bay have apparently environmental pollution problems, such as eutrophication, red tide, and hypoxia. The carrying capacity of the Bay is estimated by hydrodynamic model and ecosystem model, material circulation including bivalve in ecosystem is analyzed by the growth model of bivalve. The resulting reduction in the input load was found to be 50~90%, which is unrealistic. When the efficiency of water quality improvement through bivalve farming was assessed based on the autochthonous COD, 30.7% of the total COD was allochthonous COD and 69.3% was autochthonous COD. The overall autochthonous COD reduction rate by bivalve aquaculture farm was found to be about 6.7%. This study indicate that bivalve farming is about 31% less expensive than advanced treatment facilities that remove both nitrogen and phosphorous.