As storm-driven coastal flooding increases under climate change, wetlands such as saltmarshes are held as a nature-based solution. Yet evidence supporting wetlands’ storm protection role in estuaries—where both waves and upstream surge drive coastal flooding—remains scarce. Here we address this gap using numerical hydrodynamic models within eight contextually diverse estuaries, simulating storms of varying intensity and coupling flood predictions to damage valuation. Saltmarshes reduced flooding across all studied estuaries and particularly for the largest—100 year—storms, for which they mitigated average flood extents by 35% and damages by 37% ($8.4 M). Across all storm scenarios, wetlands delivered mean annual damage savings of $2.7 M per estuary, exceeding annualised values of better studied wetland services such as carbon storage. Spatial decomposition of processes revealed flood mitigation arose from both localised wave attenuation and estuary-scale surge attenuation, with the latter process dominating: mean flood reductions were 17% in the sheltered top third of estuaries, compared to 8% near wave-exposed estuary mouths. Saltmarshes therefore play a generalised role in mitigating storm flooding and associated costs in estuaries via multi-scale processes. Ecosystem service modelling must integrate processes operating across scales or risk grossly underestimating the value of nature-based solutions to the growing threat of storm-driven coastal flooding.