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Tokyo Bay is one of the estuaries in Japan with a high population of almost 26 million people in the basin area. One of the major concerns for the environment in this water area is the decreasing ecosystem functions including the deterioration of water and sediment qualities caused by various anthropogenic activities. Since the bottom sediments around almost the entire area of the inner bay consist of fine materials with a high organic content, which cause the deterioration of water quality through processes such as hypoxia, an understanding of the fine sediment dynamics in the Bay is crucial for an environmental assessment of the water area. This paper proposes a model for the key processes of fine sediment dynamics, which reflects field data about muddy bed structures and their dynamics obtained during the monitoring campaign in 2007. One of the specific features of the sediment in the Bay at present is the persistent existence of fluid mud layers (water content over 300 %) with a thickness of around a few decimeters, which might be caused by deposition of abundant organic particles due to eutrophication. The present study shows that diffusion flux model delivers quite reliable results for estimating erosion flux from the top of fluid mud layers after calibrating the model parameter against the time series data of vertical flux measured by an acoustic Doppler velocimeter system. This study also derives analytical solutions, based on the Bingham fluid concept, of advection flux in the fluid mud layer on which external shear stress force is applied. [ABSTRACT FROM AUTHOR]