Accumulation of soft mud (muck) at the head of Tokyo Bay is one of the major causes of deterioration of water quality and ecosystems. We conducted field observation of sediment quality and numerical simulation of grain size distribution to reveal the mechanism of its accumulation, which will provide a suggestion for the future restoration of its estuarine environment. We revealed the detailed variation in sediment quality and one of the causes is attributed to the lower decomposition rate of organic matter due to the long-term exposure to hypoxic waters along with the higher rate of accumulation of very fine particles reflecting hydrodynamic properties.