In this study, in order to clarify the mechanism of hypoxia occurring in the northern part of Isahaya Bay during summer season, a multiple regression analysis was conducted by using dissolved oxygen (DO) in bottom layer and water quality data. The results indicated that DO in bottom layer had a negative correlation with water temperature (difference between surface layer and bottom layer), salinity (difference between bottom layer and surface layer), and surface layer's chlorophyll-a (data collected 12 hours before). Especially, it has been proved that a difference between surface layer and bottom layer in water temperatures could have a major influence on the dynamic behaviors of DO in bottom layer. Moreover, the phenomenon at the observation tower B4 was affected by the water depth which a thermocline was formed. Furthermore, based on the tidal current and DO sequential data, near Kamachiku's waterfront, it was confirmed that hypoxic water occurred. This hypoxic water occurrence was due to the consumption of DO that inflowed from the bottom layer water column near observation tower B4.