The present study investigated the levels of As, Cd, Cr, Cu, Hg, Mn, Ni, Pb and Zn in the seagrasses Posidonia oceanica and Cymodocea nodosa, and in the wetland macrophytes Phragmites australis, Arundo donax, Typha domingensis, Apium nodiflorum, and Nasturtium officinale. Results showed that the bioaccumulation capacity from sediments, translocation, total levels in plant tissues, and bioindication of metals in sediments, are generally species-specific. In particular, the patterns of metals in the aquatic plants studied were overall independent of ecology (coasts vs wetlands), biomass, anatomy (rhizomatous vs non rhizomatous plants), and life form (hemicrytophytes vs hydrophytes). However, marine phanerogams and wetland macrophytes shared some characteristics such as high levels of heavy metals in their below-ground organs, similar capacity of element translocation in the rhizosphere, compartmentalization of metals in the different plant organs, and potential as bioindicators of Cu, Mn and Zn levels in the substratum. In particular, the present findings indicate that, despite ecological and morphological similarities, different plant species tend to respond differently to exposure to heavy metals. Furthermore, this seems to result from the species individual ability to accumulate and detoxify the various metals rather than being attributed to differences in their ecological and morpho-anatomical characteristics. Display omitted •Plants respond differently to metal inputs, despite similar ecology and anatomy.•Bioaccumulation, internal translocation and bioindication are species-specific.•Total metal concentrations are generally species-specific.•Plants share high metal levels in roots and organ element compartmentalization.•P. australis was the best bioaccumulator and bioindicator species.