Submersed aquatic vegetation is an important modulator of sediment delivery from the Susquehanna River through the Susquehanna Flats into the Chesapeake Bay. However, the impact of vegetation coupled with the physical drivers of sediment transport through the region are not well understood. This study used a new vegetation component in a coupled flow-wave-sediment transport modeling system (COAWST) to simulate summer through fall 2011, when the region experienced a sequence of events including Hurricane Irene and Tropical Storm Lee. Fine sediment was exported under normal flows and high wind forcing but accumulated under high flows. The relative effect of vegetation under normal and high wind forcing depended on previous sediment dynamics. Vegetation doubled the accumulation of fine sediments under high flows. While further refinement of the bed model may be needed to capture some nuances, the COAWST modeling system provides new insights into detailed sediment dynamics in complex vegetated deltaic systems.