Forecasting salinity in an estuary reservoir is essential to promise irrigation water for the reclaimed land. The objective of the research was to assess salinity balance and its temporal and spatial variations in the Iwon estuary reservoir which has been issued by its high contents of salinity in spite of desalination process for four years. Seepage flows through the see dikes which could be one of possible reason of high salinity level of the reservoir was calculated based on the salinity balance in the reservoir, and used as input data for salinity modeling. A three-dimensional hydrodynamic model, Environmental Fluid Dynamics Code (EFDC), was used to simulate salinity level in the reservoir. The model was calibrated and validated based on weekly or biweekly observed salinity data from 2006 to 2010 in four different locations in the reservoir. The values of $R^2$, RMSE and RMAE between simulated and observed salinity were calculated as 0.70, 2.16 dS/m, and 1.72 dS/m for calibration period, and 0.89, 1.15 dS/m, and 0.89 dS/m for validation period, respectively, showing that simulation results was generally consistent with the observation data.