Sediment transport in the Hangzhou Bay is extremely complicated due to its bathymetry and hydrodynamic conditions. The ECOMSED model is employed to simulate three-dimensional (3-D) cohesive sediment transport in Hangzhou Bay. Dynamical factors such as Coriolis force, tides, salinity, river discharges, and waves are considered in the model. The wave parameters, including the significant wave height, period, and direction, are calculated with the SWAN model. The Grant-Madsen model is introduced for the bed shear stress due to the combined effect of waves and currents. The formulation of bed shear stress used to calculate the sink/source terms is modified based on previous research that sufficiently validated the formulation with measurement data. The integrated model of the above-mentioned models is applied to simulate sediment transport in Hangzhou Bay. The results of the simulation agree well with field observations concerning the distribution of suspended sediment, indicating that the sediments are remarkably suspended in Hangzhou Bay under the action of waves and currents.