In European salt marshes, recent invasions by the grass Elymus cithericus raise questions regarding subsequent habitat modification and its effects on the resident biota. In this study, we studied the effects of modified salt-marsh structure on occurring spider assemblages, especially on salt exposure and flood resistance. We showed that locations having tall and deep-rooted invasive vegetation contained more species able to resist tidal floods as compared with locations with natural vegetation. Dominant species displayed different temporal trends between habitat types after flooding, with some species being less affected by floods either in invaded or in natural habitats. Some cursorial species were able to (re)colonize salt marshes after a spring flood as salinity levels decreased. Finally, stand characteristics of E. athericus did not affect the distribution of halotolerant spiders. As a habitat structure relates to flood resistance and/or risk-avoiding strategies, our results indicate that the status of salt-marsh resident species should be considered according to their habitat affinity.