It is essential for port planning, coastal zone management and environmental impact study to analyze the variation of current and water quality due to the development of water area and discharged water from estuary barrage and basin etc. Mokpo sea area downstreams from a long river and two large basins, the Yongsan river and Yongam-Kumho basins discharging much of water through water gates for the purpose of flood control and prohibition of salt intrusion to the inland fresh water area. In this study, the numerical calculations were carried out for the analysis of diffusion characteristics due to discharging operation, adapting the results of tidal current simulation ADI methord is applied to the governing equation for the movement of sea water and diffusion and 6-point method to the advection terms of diffusion equation. As the results of this study, it is known that the discharging operation causes increasing and/or decreasing of current velocity and enlarging and/or depressing of pollutant diffusion limits depending on the distance from the discharging gates and the mode of discharging operation. To utilize these result, the linked gate operation and the method increasing exchange of sea water must be considered.