Widespread land use change in coastal ecosystems has led to a decline in the amount of habitat available for fish and wildlife, lower production of ecosystem goods and services, and loss of recreational and aesthetic value. This has prompted global efforts to restore the natural hydrologic regimes of developed shorelines, especially resource-rich estuaries, but the resilience of these restored ecosystems in the face of accelerated sea-level rise (SLR) remains uncertain. We implemented a Monitoring-based Simulation of Accretion in Coastal Estuaries (MOSAICS) in R statistical software to address uncertainty in the resilience of modified estuarine habitats, using the Nisqually River Delta in the Pacific Northwest USA as a case study. MOSAICS is a spatially explicit model with a numerical foundation that uses empirical monitoring datasets to forecast habitat change in response to rising tidal levels. Because it accounts for the crucial ecomorphodynamic feedbacks between tidal inundation, vegetative growth, and sediment accretion, MOSAICS can be used to determine whether alternative management scenarios, such as enhanced sediment inputs, will bolster estuarine resilience to SLR. Under moderate SLR (0.62 m), the model predicted that a two-fold increase in mean daily suspended sediment during the rainy season was sufficient to maintain Nisqually’s emergent marshes through 2100, but under high SLR (1.35 m) MOSAICS indicated that greater sediment additions would be necessary to prevent submergence. A comparison between a restored marsh with subsided and high-elevation areas and a relict marsh demonstrated that the subsided restoration area was highly susceptible to SLR. Findings from the MOSAICS model highlight the importance of a site’s initial elevation, capacity for producing above and belowground biomass, and suspended sediment availability when considering management actions in estuaries and other coastal ecosystems.