Intertidal wetlands provide vital habitat for numerous species by serving as a basal resource and refuge for shelter-seeking fauna. These environments are particularly important for transient nekton that trophically link marine and terrestrial food webs via migration into the intertidal during the flooding tide. Changes in coastal vegetation due to a warming climate, such as the replacement of temperate saltmarshes with tropical mangroves, may alter habitat use by transient species due to differences in food provisioning and the structural attributes of mangrove and saltmarsh vegetation. In northeast Florida (USA), Fundulus heteroclitus (mummichog) and F. majalis (striped killifish) are abundant, trophically important, transient fishes that may exhibit behavioral changes with coastal habitat shifts. We experimentally manipulated predator presence in a large-scale mesocosm containing an array of 4 habitats found at the mangrove-saltmarsh ecotone: marsh vegetation (smooth cordgrass Spartina alterniflora), 2 species of mangroves (red mangrove Rhizophora mangle and black mangrove Avicennia germinans), and sand, and measured prey fish habitat use and schooling dynamics. Mummichogs utilized black mangrove habitat to the same degree as cordgrass regardless of the presence of a predator, indicating that mummichogs perceive both habitats as providing equivalent protection. Killifish exhibited little affinity for any particular habitat and exhibited schooling behavior over seeking refugia for predator avoidance, suggesting that vegetation changes may have little effect on killifish behavior. Further research on how such patterns of habitat use combined with habitat-specific dietary constituents of fundulids will help to predict how saltmarsh loss at the ecotone will influence nutrient and energy flows in coastal food webs.