The increasing rate of sea level rise (SLR) poses a major threat to coastal lands and natural resources, especially affecting natural preserves and protected areas along the coast. These impacts are likely to exacerbate when combined with storm surges. It is also expected that SLR will cause spatial reduction and migration of coastal wetland and marsh ecosystems, which are common in the natural preserves. This study evaluates the potential impacts of SLR and marsh migration on the hydrodynamics and waves conditions inside natural protected areas during storm surge. The study focused on four protected areas located in different areas of the Chesapeake Bay representing different hydrodynamic regimes. Historical and synthetic storms are simulated using a coupled storm surge (ADCIRC) and wave (SWAN) model for the Bay region for current condition and future scenarios. The future scenarios include different rates of local SLR projections (0.48 m, 0.97 m, 1.68 m, and 2.31 m) and potential land use changes due to SLR driven marsh migration, which is discretized in the selected preserve areas in a coarse scale. The results showed a linear increase of maximum water depth with respect to SLR inside the protected areas. However, the inundation extent, the maximum wave heights, and the current velocities inside the coastal protected areas showed a non-linear relationship with SLR, indicating that the combined impacts of storm surge, SLR, and marsh migration depend on multiple factors such as storm track, intensity, local topography, and locations of coastal protected areas. Furthermore, the impacts of SLR were significantly greater after a 1 m threshold of rise, suggesting the presence of a critical limit for conservation strategies.