Sea Level Rise (SLR) caused by climate change is impacting coastal wetlands around the globe. Due to their distinctive biophysical characteristics and unique plant communities, freshwater tidal wetlands are expected to exhibit a different response to SLR as compared with the better studied salt marshes. In this study we employed the Sea Level Affecting Marshes Model (SLAMM), which simulates regional- or local-scale changes in tidal wetland habitats in response to SLR, and adapted it for application in a freshwater-dominated tidal river system, the Hudson River Estuary. Using regionally-specific estimated ranges of SLR and accretion rates, we produced simulations for a spectrum of possible future wetland distributions and quantified the projected wetland resilience, migration or loss in the HRE through the end of the 21(st) century. Projections of total wetland extent and migration were more strongly determined by the rate of SLR than the rate of accretion. Surprisingly, an increase in net tidal wetland area was projected under all scenarios, with newly-formed tidal wetlands expected to comprise at least 33% of the HRE's wetland area by year 2100. Model simulations with high rates of SLR and/or low rates of accretion resulted in broad shifts in wetland composition with widespread conversion of high marsh habitat to low marsh, tidal flat or permanent inundation. Wetland expansion and resilience were not equally distributed through the estuary, with just three of 48 primary wetland areas encompassing >50% of projected new wetland by the year 2100. Our results open an avenue for improving predictive models of the response of freshwater tidal wetlands to sea level rise, and broadly inform the planning of conservation measures of this critical resource in the Hudson River Estuary.