Salt marshes are ecologically and physically essential habitats in coastal intertidal flats. In addition to providing nursery grounds for various wildlife, vegetation in marshes acts as a buffer zone that slows flooding waters. Extensive marsh platforms can also attenuate wave energy to protect coastal communities. Complex geometries make it challenging for models to capture the spatiotemporal variabilities in the transport of lateral water and sediment over tidal creek-marsh complexes. To study water exchange processes between tidal creeks and marshes, field observations were conducted within tidal creeks in the Chongming Dongtan Shoal of the Changjiang Estuary, an area dominated by Phragmites australis, Scirpus mariqueter, and Spartina alterniflora. A coupled wave-current-sediment-vegetation model that parameterized the three vegetation species was developed and applied to the tidal creek complex of Chongming Dongtan. Validated with the observational data, the modeling results were used to examine the influence of vegetation on flooding/draining processes within tidal creeks and mudflats. The model showed that vegetation not only modified the flow pattern at high tide in the high-elevation marsh but also significantly intensified the tidal flows in tidal creeks in the low-elevation regions. Both the observations and model detected significant transport of water and sediment from the marsh to tidal creeks, seaward sediment export over tidal cycles. The simulated salinity exhibited a considerable spatial gradient, matching well with the salt tolerances of the major vegetation types. This model can be potentially used to determine how future scenarios of hydrodynamics could affect vegetation zonation.