Both submerged aquatic vegetation and salt marsh are important coastal ecosystems known for their effectiveness in sediment trapping and carbon burial. However, their proximity can lead to competition for limited sediment resources, potentially compromising their capacity to facilitate sufficient sediment deposition to withstand sea-level rise. Here we applied the Delft3D flow and sediment transport model in a shallow coastal bay to assess how seasonal variations in seagrass density and storms modulate sediment retention and connectivity between subtidal flats and intertidal marsh. Results show that submerged seagrass meadows acted as temporary storage for fine sediment and altered the timing of sediment transport to an adjacent marsh through seasonal growth cycles. When seagrass occupied subtidal flats, sediment flux to the marsh was controlled by seasonal seagrass density variations, with peak fluxes during winter senescence. In contrast, wave-induced sediment resuspension on the flats was the major contributor for marsh sediment input in the simulation with no seagrass, with peak storm-driven fluxes in summer/autumn. Overall, seagrass meadows significantly increased annual sediment accumulation on the vegetated subtidal flats by tenfold, while reducing annual marsh sediment flux and edge erosion by 20%. Seagrass meadows and marsh were both able to maintain a sediment deposition rate comparable to the rapid sea-level rise at the study site despite the absence of terrestrial sediment sources. Our findings highlight the strong seasonal control subtidal aquatic vegetation has in the vertical and horizontal dynamics of tidal flat-marsh systems and provide insights that can inform wetland restoration and management strategies in similar systems. [ABSTRACT FROM AUTHOR]