In order to figure out hydrodynamic and water quality changes after completion of dike construction of the Saemangeum, which behaves as a semi-enclosed estuarine lake, numerical simulations based on fine grid structure by using EFDC were intensively carried out. In this study some limitations of precedent study has been improved and gate operation were considered. Also 3 phases such as air-water-sediment interaction modeling was considered. It is clear that inner mixing of the Saemangeum is dominated by Mankyeong and Dongjin riverine discharges rather than the gate opening influence through the Lagrangian particle tracking simulations. Vertical DO structure after the dike completion shows steep gradient especially at Dongjin river estuary due to lessen of outer sea water exchange. Increasing SOD at stagnantly changed man-made reservoir might cause oxygen deficiency and accelerating degradation of water quality. According to TSI evaluation test representing eutrophication status, it shows high possibility of eutrophication along Mankyeong waterway in spite of dike completion, while the index is getting high after final closing along Dongjin waterway. Numerical tests with gate operations show significant differences in water quality. Thus it should be noted that proper gate operation plays a major role in preserving target water quality and management for inner development plan.