Abstract Cymodocea nodosa is a common seagrass species of shallow and sheltered Mediterranean waters, where extreme flushing of plumes can occur during excessive rainfall. Cymodocea nodosa shoots were sampled from two habitats of Kavala Gulf, one nearly pristine (less stressed, Vrasidas) and another highly stressed (Nea Karvali), to study if flooding might negatively affect seagrass habitats. Photosynthetic performance of shoots from the pristine habitat acclimated better than shoots from highly stressed conditions simulating a flooding event. Indeed, a significant (p < 0.01) interaction between habitat and flooding on photochemical energy harvesting (ΔF/Fm′) values was found, with lower ΔF/F m′ values in the pristine habitat under control conditions. Furthermore, based on relative electron transport rate (rETR) curves reconstructed from fluorescence-versus-irradiance data, shoots from the pristine habitat performed better after 18 days of treatment to flooding. On the other hand, shoots from highly stressed habitats grew faster than pristine ones, but their growth decreased similarly under flooding conditions. The implications for management and conservation priorities for this phenotypically plastic seagrass in the Mediterranean are discussed.