An investigation of the water mass and surface sediments was conducted in 2004 to clarify the cause of mass mortalities of ark shell (Scapharca kagoshimensis) that have occurred during summer of recent years in the northwestern part of Ariake Bay. In May, a hypoxia event had already been observed near the bottom in the marginal area of the mudflat, where the surface sediment was oxygenated. A red tide was observed simultaneously with the hypoxia event, suggesting that oxygen consumption occurred due to the decomposition of organic matter originating from the red tide phytoplankton in the bottom layer. Since the end of June, a continuous occurrence of red tides and enhancement of the stratification caused frequent hypoxia events, and then intrusion of low oxygen water from offshore enhanced the hypoxia in the marginal area of the mudflat, resulting in the highly reducing conditions in the surface sediments after July. Hydrogen sulfide was considered to be formed due to the decomposition of red tide phytoplankton and/or dead benthos including ark shell under the anaerobic-reducing conditions, which enhanced the hypoxia. The more ark shells died in the surface sediments, the more hydrogen sulfide would be generated from the surface sediments. The large amount of hydrogen sulfide generated under such reducing conditions could have induced large-scale anoxic water mass and also the mass mortality of ark shell in the mid and late August.