The formation of the oxygen-depleted water near the head of Ariake Bay observed in the summer of 2004 and 2005 were numerically simulated. The model reproduced oxygen-depleted water formation near the head of the bay well. The results suggested that oxygen-depleted water was formed in the following processes. First, formation of oxygen-depleted water occurred just after big discharges from rivers due to strong salinity stratification and massive Skeletonema sp. growth. Second, dissolved oxygen in the bottom water was depleted in August when no big discharge was observed, and higher temperature was kept. In this period, thermal stratification was developed, and Chattonella sp. grew rapidly because they can vertically migrate and uptake nutrients in the bottom layer.