Muddy sediments with high water content are often observed at near surface of the sea bottom in enclosed bays and estuaries, where fine suspended sediments are abundant in the water. Since transport process of the muddy sediments is one of the crucial factors for near-bed water quality and habitat conditions of benthic organisms, the process was modeled under the consideration of the characteristics of muddy sediments in the field. The field monitoring of sediment qualities by core sampling have been conducted around the mouth of the Tama River mouth in Tokyo Bay and the data shows that very soft mud with high water content of over 400 % is prevailing in the deeper area. A monitoring campaign in the summer of 2007 with measurements of near bottom current and turbidities revealed dynamical sediment transport processes under the energetic wave and current condition due to a passage of typhoon. Through the sediment budget analysis during the typhoon event, it is shown that bed load transport is crucial for the bed level change in addition to the vertical transport including erosion and deposition fluxes. Key processes of the muddy sediment transport such as resuspension and horizontal movement of observed fluid mud layer was modeled. Resuspension flux is estimated as turbulent diffusion flux between the sea water and fluid mud layer and estimation results show fairly good agreement with observed data. For the horizontal flux estimation, the mass flux in the fluid mud layer was analytically calculated using the relationship between shear stress and deformation rate for Bingham fluids considering the vertical structure of sediments or yield stress profile in the observed fluid mud layer.