In Jinhae-Masan bay, a typical semi-dosed bay in Korea, the water quality is severely deteriorated because of the dosed topographic character and the inflow of nutrients from the land. There have been attempts to apply a water quality model dealing with the entrophication phenomenon and the oxygen-deficient mass in the bay in summer, but there have been few examples of models that have considered the phenomenon of stratification in the proper order, and then it is performed the model of water quality. Therefore, this study collected and analyzed the pre-observed water temperature data from Jinhae-Masan bay in summer and then constructed a density model using the topographic heat accumulation effect and inflow from the river to examine the temperature stratification. The simulation results show that this model could demonstrate the temperature stratification in the Jinhae-Masan bay very well.