Seagrasses are marine flowering plants that provide key ecological services. In recent decades, multiple stressors have caused a worldwide decline in seagrass beds. Changes in bottom friction associated with seagrass loss are expected to influence the ability of estuarine systems to trap sediment inputs through local and regional changes in hydrodynamics. Herein, we conduct a numerical study using six historical maps of seagrass distribution in Barnegat Bay, USA, to demonstrate that reductions in seagrass coverage destabilize estuarine systems, decreasing their flood-dominance in the areas interested by seagrass disappearance and increasing bed-shear stress values across the entire back-barrier basin. Furthermore, we reveal how seagrass decline has considerably increased the impact of wind-waves on marsh edges between 1968 and 2009. From a comparison with a numerical experiment without submerged aquatic vegetation, we estimate that up to 40% of the computed wave thrust on marsh boundaries can be reduced by seagrass beds and we find that the location of a seagrass patch in addition to its aerial extent plays a crucial role in this attenuation process. This study highlights the benefits of seagrass meadows in enhancing estuarine resilience and reducing marsh-edge retreat by wind-wave attack, which is recognized as a chief agent in lateral marsh loss.