Two distinct microtidal estuarine systems were assessed to advance the understanding of the coastal dynamics of sea level rise in salt marshes. A coupled hydrodynamic-marsh model (Hydro-MEM) was applied to both a marine-dominated (Grand Bay, Mississippi) and a mixed fluvial/marine (Weeks Bay, Alabama) system to compute marsh productivity, marsh migration, and potential tidal inundation from the year 2000 to 2100 under four sea level rise scenarios. Characteristics of the estuaries such as geometry, sediment availability, and topography, were compared to understand their role in the dynamic response to sea level rise. The results show that the low sea level rise scenario (20 cm) approximately doubled high-productivity marsh coverage in the marine-dominated estuary by the year 2100 due to an equilibrium between the rates of sea level rise and marsh platform accretion. Under intermediate-low sea level rise (50 cm), high-productivity marsh coverage in the year 2100 increased (doubled in the marine-dominated estuary and a seven-fold increase in the mixed estuary) by expanding into higher lands followed by the creation of interior ponds. The results also indicate that marine-dominated estuaries are vulnerable to collapse as a result of low, relatively uniform topography and lack of sediment sources, whereas mixed estuaries are able to expand due to higher elevations and sediment inputs. The results from the higher sea level rise scenarios (the intermediate-high (120 cm) and high (200 cm)) showed expansion of the bays along with marsh migration to higher land, producing a five-fold increase in wetland coverage for the mixed estuary and virtually no net change for the marine-dominated estuary. Additionally, hurricane storm surge simulations showed that under higher sea level rise scenarios, the marine-dominated estuary demonstrated weaker peak stage attenuation indicating that the marsh’s ability to dissipate storm surge is sensitive to productivity changes and bay expansion / marsh loss.