This study evaluates, on a preliminary basis, the principal morpho-physiological effects induced by pollution stress in four aquatic vegetation species of great ecological relevance in transitional water ecosystems. Three macroalgae (Chaetomorpha linum, Valonia aegagrophyla, Graciliariopsis longissima) and one phanerogams species (Ruppia cirrhosa) were exposed to different doses of trace elements (Cu, Hg, Zn) and surfactants (dodecylbenzenesulfonic acid sodium salt) in laboratory controlled microcosm conditions and morpho-physiological responses (photosynthetic complex alteration, percentage of died cells, morphological changes) were measured before and after 7 and 14 days of exposure. Levels of pollutants in tissues and BioConcentration Factors (BCF) for each species were calculated after 14 days of exposure. Results suggest that photosynthetic complex alteration can be a useful tool to evaluate early and sub-lethal significant changes due to exposure to pollution stress in all of the considered species. A clear species-specificity was observed concerning trace element levels in tissues after 14 days of exposure, while dose-dependent behavior was observed for BCFs.