Coral reefs form complex physical structures that can help to mitigate coastal flooding risk^1,2. This function will be reduced by sea-level rise (SLR) and impaired reef growth caused by climate change and local anthropogenic stressors³. Water depths above reef surfaces are projected to increase as a result, but the magnitudes and timescales of this increase are poorly constrained, which limits modelling of coastal vulnerability^4,5. Here we analyse fossil reef deposits to constrain links between reef ecology and growth potential across more than 400 tropical western Atlantic sites, and assess the magnitudes of resultant above-reef increases in water depth through to 2100 under various shared socioeconomic pathway (SSP) emission scenarios. Our analysis predicts that more than 70% of tropical western Atlantic reefs will transition into net erosional states by 2040, but that if warming exceeds 2 °C (SSP2–4.5 and higher), nearly all reefs (at least 99%) will be eroding by 2100. The divergent trajectories of reef growth and SLR will thus magnify the effects of SLR; increases in water depth of around 0.3–0.5 m above the present are projected under all warming scenarios by 2060, but depth increases of 0.7–1.2 m are predicted by 2100 under scenarios in which warming surpasses 2 °C. This would increase the risk of flooding along vulnerable reef-fronted coasts and modify nearshore hydrodynamics and ecosystems. Reef restoration offers one pathway back to higher reef growth^6,7, but would dampen the effects of SLR in 2100 only by around 0.3–0.4 m, and only when combined with aggressive climate mitigation.