Estuarine systems that provide valuable ecosystem services to society and important foraging and rearing habitat for fish and wildlife species continue to undergo degradation. In Puget Sound, WA, as much as 70–80% of historic estuarine habitat has been lost to anthropogenic development, and continued losses are expected through the end of the twenty-first century due to rising sea levels. To evaluate whether Puget Sound’s estuarine habitats will keep pace with current and projected sea-level rise (SLR), we assessed vertical rates of elevation change from a regional network of surface elevation tables and marker horizons (SET-MH). Over the past two decades, SET-MH equipment has been installed throughout a variety of habitats in five Puget Sound estuaries: the Nisqually, Snohomish, Stillaguamish, and Skagit River estuaries, and Padilla Bay. These data provide a unique opportunity to assess elevation change and habitat resilience across a spatiotemporal and environmental gradient. We observed different rates of surface elevation change among estuaries and habitats (Nisqually = 4.64 ± 2.81 mm/year, Snohomish = 5.71 ± 5.83 mm/year, Stillaguamish = 12.82 ± 10.29 mm/year, Skagit = 16.13 ± 7.57 mm/year, Padilla =  − 1.25 ± 1.58 mm/year). The highest rates were found at restoring sites with regular sediment input in the Stillaguamish and Skagit estuaries, whereas rates were consistently negative at low elevation sites in sediment starved Padilla Bay. Many sites in Puget Sound appear to be keeping pace with current rates of relative SLR, and some areas are on track to exceed projected rates through the end of the century. These findings indicate that Puget Sound’s estuarine habitats can be resilient to rising tidal levels—as long as sediment delivery is maintained.