Vegetated salt marsh habitats are widely considered critical for supporting many species of nekton, yet direct evidence of the processes controlling marsh habitat use for most species remains elusive. We related salt marsh flooding patterns and nekton trophic dynamics among 14 sites spanning 2500 km across the northern Gulf of Mexico (GoM) and southern Atlantic coasts of the USA. Functional access for nekton to marsh vegetation (edge flooded to =5 cm depth) ranged from <40% of the time at some central GoM sites to >90% access in the western GoM and Pamlico Sound. Food web mixing models based on stable isotope analysis show that the importance of Spartina trophic support for common nekton may be regulated by the duration of marsh surface flooding. In particular, the potential contribution of Spartina production was positively related to indices of marsh surface flooding for brown shrimp Farfantepenaeus aztecus, white shrimp Litopenaeus setiferus, small (=60 mm carapace width) blue crabs Callinectes sapidus, grass shrimp Palaemonetes pugio, and killifish Fundulus heteroclitus/grandis. The value of Spartina salt marsh production to several common species of nekton appears to depend, at least in part, on direct access to the vegetated marsh surface, which is regulated by hydrodynamics. Hence, the substantial geographic and temporal variability in marsh flooding regulates the functional roles and value of these tidal wetlands for aquatic organisms.