Abstract Salt marsh vulnerability to sea‐level rise (SLR) is typically assessed using point measurements of vertical accretion, neglecting three‐dimensionality of geomorphic evolution and spatial variability. Recent studies suggest links between vertical and horizontal vulnerability, with differences between oligohaline and polyhaline marshes, yet these relationships remain untested in estuary‐marsh systems. Here we combine geospatial analysis with hydrodynamic modeling to evaluate how unvegetated/vegetated marsh ratio (UVVR), a metric of marsh degradation, relates to elevation across hydrological regions and salinity regimes in the Albemarle‐Pamlico Estuarine System, the largest lagoonal estuary in U.S. We show that at given normalized elevation, UVVR decreases across hydrological regions and salinity regimes from offshore to inland. UVVR‐elevation relationship varies systematically with both hydrological setting and salinity regime, with hydrology exerting stronger influence. These findings challenge the assumption of a universal marsh deterioration trajectory and underscore the need to account for spatial heterogeneity when predicting responses to SLR.