This paper presents the modeling of mud accumulation in Tokyo Bay. The model consists of hydrodynamic, wave hindcasting, bed shear stress and multi-class sediment sub-models in order to simulate the sediment associated processes both in the water body and bed layer. The present model accounts for sediment transport, settling, deposition, resuspension, accumulation and burial sedimentation processes, and it is capable to reproduce the accumulation of muddy sediments. Following the concept of multi-class particle model, the bed characteristics, i.e. the spatial distributions of particle size and the water content ratio in bed materials, were computed and qualitatively verified with field investigation data. The computed spatial variation in mud accumulation rate, particle size distribution and water content ratio were consistent with field data. Some discrepancies were identified and discussed.