To test a hypothesis that the development of the stratification of water enhances the phytoplankton blooming and hypoxia without any increase in the nutrient loading in an enclosed bay, the present study examines the spatial relationship among the hydrographic structures, physico-chemical conditions of the sediments, and macrobenthic communities at 21 stations in the inner part of Ariake Bay, Kyushu, Japan in August 2010, and compares the distribution of the mud content of the sediment in 2014 with those of last few decades focusing on the succession of sedimentary environment. The stratification of water developed in the innermost part of Ariake Bay, and hypoxia occurred below the well-stratified water. The distribution of the muddy bottom with high content of organic matter derived from phytoplankton almost overlapped with the stratified water. Cluster analysis concerning the grain size composition of the sediment corresponded greatly to that of the macrobenthic communities. These results indicate that the development of the stratification of water strongly influences the sedimentary environments and the community structure of macrobenthic animals in the inner part of Ariake Bay. Comparison with the past distribution of mud content revealed eastward expansion of the muddy sediment, and it suggests the distribution of the well-stratified water has expanded recently. The results of the present study show the possibility that the development of the stratified water causes a series of phenomena, which closely resemble ones following the development of the eutrophication of the water, without any increase in the nutrient loading in an enclosed bay or estuary.