Seagrasses are marine flowering plants that strongly impact their physical and biological
surroundings and are therefore frequently referred to as ecological engineers. The effect of seagrasses on coastal bay resilience and sediment transport dynamics is understudied. Here we use six historical maps of seagrass distribution in Barnegat Bay, USA, to investigate the role of these vegetated surfaces on the sediment storage capacity of shallow bays. Analyses are carried out by means of the Coupled-Ocean-Atmosphere-Wave-Sediment Transport (COAWST) numerical modeling framework. Results show that a decline in the extent of seagrass meadows reduces the sediment mass potentially stored within bay systems. The presence of seagrass reduces shear stress values across the entire bay, including unvegetated areas, and promotes sediment deposition on tidal flats. On the other hand, the presence of seagrasses decreases suspended sediment concentrations, which in turn reduces the delivery of sediment to marsh platforms. Results highlight the relevance of seagrasses for the long-term survival of coastal ecosystems, and the complex dynamics regulating the interaction between subtidal and intertidal landscapes.