A semi-closed estuary, Ohmura Bay, consists of two parts characterized by geographic and oceanographic features. One is a deep and vertically well-mixed area near the mouth of the bay; the other is a shallower, rather fiat and stratified area. A second thermocline and oxygen-deficient water are usually formed in the bottom layer of the latter stratified area in summer. We observed temperature and salinity profiles at 18 points over Ohmura Bay from June to September once or twice a month in 1994. To examine the physical processes in the evolution of stratified structure, numerical experiments were carried out, and the structures of the tidal residual current and density current based on the data observed in July, August and September were obtained. The results showed that the tidal residual current would not have much influence on the circulation in the stratified area of the bay. On the other hand, the density current generated by the horizontal difference of stratification intrudes into the stratified area of the bay. The level of intrusion depends on the structure of stratification. In July and August, the mixed water in the bay-mouth area intrudes into the intermediate layer of the stratified area. Therefore, the bottom water in the stratified area is isolated from the intruded high-oxygen and high temperature water, resulting in formation of a distinct second thermocline, In September, the stratification is weakened, and the water in the mouth area flows into the bottom layer of the stratified area, the low-oxygen and low temperature water is pushed out from the central part of the stratified area; then, the second thermocline disappears.