Accurate prediction of sediment transport in coastal waters requires considering the effects of wind waves on current velocity and bottom shear stress. A 3D numerical model was developed to predict sediment transport rates, accounting for bed-load transport, suspended load sediment transport within the wave boundary layer, and suspended load sediment transport above the wave bottom boundary layer. Wind wave effects were included in the model through analytical models. Results show that wind waves can significantly impact sediment mobilization in coastal scenarios, and stratification can affect the transport rates of fine sediments.