The EFDC (Environmental Fluid Dynamics Code), a numerical model for simulating three-dimensional (3D) flow, transport, and biogeochemical processes in surface water systems including rivers, reservoirs, and estuaries, was applied to assess the effect of sea water and fresh water exchange rates ($Q_e$) on the mixing characteristics of a conservative pollutant (tracer) induced from upstreams and salinity in Saemangeum Lake, Korea. The lake has been closed by a 33 km estuary embankment since last April of 2006, and now seawater enters the lake partially through two sluice gates (Sinsi and Garyuk), which is driving the changes of hydrodynamic and water quality properties of the lake. The EFDC was constructed and calibrated with surveyed bathymetry data and field data including water level, temperature, and salinity in 2008. The model showed good agreement with the field data and adequately replicated the spatial and temporal variations of the variables. The validated model was applied to simulated the tracer and salinity with two different gate operation scenarios: RUN-1 and RUN-2. RUN-1 is the case of real operation condition ($Q_e=25,000,000;m^3$) of 2008, while RUN-2 assumed full open of Sinsi gate to increase $Q_e$ by $120,000,000;m^3$. Statistical analysis of the simulation results indicate that mixing characteristics of pollutants from upstream can be significantly affected by the amount of $Q_e$.