This study simulated water quality item and flow rate of subbasin for Saemangeum watershed using Soil and Water Assessment Tool (SWAT) model and Environmental Fluid Dynamics Code (EFDC) model which simulate hydraulic and water quality in three- dimensions. The simulated values corresponded to observed value well. The result of simulation for floodgate operations at the M3 and M5 points, it exceeds water quality standard and at the M3 and D3 points, change of range for concentration is too wide, and upstream of Saemangeum reservoir is sensitive to inflow flow rate. Compared to the annual average concentration for observed station according to the discharge conditions, improvement of water quality for upstream was apparently compared to the downstream. Range of influence for change of water quality presented that maximum discharge condition, the influence range is 22 km in the direction of the Saemangeum downstream from the Mankyung bridge, and 15 km in the downstream direction of saemangeum in the Dongjin bridge. This study result demonstrated that floodgate operating at upstream has significant influence on water quality management of Saemangeum reservoir and it needs to be considered in plans of water quality management for Floodgate operation on Saemangeum reservoir.