Around the world, wetland vulnerability to sea-level rise (SLR) depends on different factors including tidal regimes, topography, creeks and estuary geometry, sediment availability, vegetation type, etc. The Plum Island estuary (PIE) is a mesotidal wetland system on the east coast of the United States. This research applied a newly updated Hydro-MEM (integrated hydrodynamic-marsh) model to assess the impacts of intermediate-low (50 cm), intermediate (1 m), and intermediate-high (1.5 m) SLR on marsh evolution by the year 2100. Model advancements include capturing vegetation change, inorganic and below and aboveground organic matter portion of marsh platform accretion, and mudflat creation. Although the results indicate a low vulnerability marsh at the PIE, the vegetation changes from high to low marsh under all SLR scenarios (2%–22%), with the higher bounds belonging to higher rise scenarios. Lower SLR produces more productive marsh (13% gain in high productivity regions), whereas the highest SLR scenario causes increased tidal inundation, which leads to loss in productivity (12% change from high to low productivity regions), generation of mudflats (17% of the domain land), and marsh migration to higher lands. Sensitive nonlinear tidal flow changes, which may be increased or decreased with SLR as a result of mudflat creation, marsh migration, and bottom friction change, emphasize the importance of integrated modeling approaches that include dynamic marsh feedbacks in hydrodynamic modeling and varying hydrodynamic effects on the marsh system.