Sea-level rise (SLR) and obstructions to sediment delivery pose challenges to the persistence of estuarine habitats and the ecosystem services they provide. Restoration actions and sediment management strategies may help mitigate such challenges by encouraging the vertical accretion of sediment in and horizontal migration of tidal forests and marshes. We used a process-based soil accretion model (Coastal Wetland Equilibrium Model) combined with a habitat classification model (MOSAICS) to estimate the effects of SLR, suspended sediment, and inland habitat migration on estuarine habitats, soil carbon accumulation, and economic value of climate change mitigation of carbon accumulation (social cost of carbon dioxide) in a macrotidal estuary in the northwest USA over 100 years (2011 to 2110). Under present-day sediment levels, we projected that after 100 years, most high salt marsh would remain with < 100 cm SLR, but substantial area converted to transitional (low) salt marsh and mudflat with ≥ 100 cm SLR. Increasing sediment availability increased the projected resilience of transitional salt marsh to SLR but did not prevent declines in high marsh area. Projected total carbon accumulation plateaued or declined with ≥ 100 cm SLR, yet the economic value of carbon accumulation continued to rise over time, suggesting that the value of this ecosystem service was resilient to SLR. Doubling or tripling sediment availability increased projected carbon accumulation up to 7.69 and 14.2 kg m⁻² and increased total economic value up to $373,000 and $710,000, respectively. Allowing marsh migration supported conversion of upland to freshwater marsh, with slight increases in carbon accumulation. These results inform climate adaptation planning for wetland managers seeking to understand the resilience of estuarine habitats and ecosystem services to SLR under multiple management strategies.