The climate change could result in the adverse effect on the estuarine system ecologically by acidifying sea water and increasing sea water temperature. Also faster temperature rise in the surface layer than the deep water strengthens the stratification and could affect the ecological system in the various ways. Therefore, the prediction of the strengthening of the stratification in an estuary will be critical in mitigating the damage to the ecosystem in the estuaries. The prediction of the stratification in the coastal water bodies needs highly resolved information of the complicate circulations near the complex estuarine coastal lines. Therefore, we downscaled data from the large-scale operational ocean models to the local regional models to simulate an estuary of Korea for the 50 years later with the sea level rise. Through this downscaled results, the stratification was quantified by the PEA. Based on the PAE analysis, the stratification effects will be much more significant in the estuarine river channel than the sea and it means that the sea level rise will affect not only the coastal water but also the upstream fresh water area.