The results of the comparative study of aquatic macrophytes from habitats with different levels and nature of anthropogenic impact - phenolic compounds (PCs) and heavy metals (HMs) have been represented in this article. The structural and functional features of Elodea canadensis Michx. photosynthetic apparatus were investigated. Plants material was collected in July, during the flowering period of macrophytes, from the background and impact areas of the Lyala and Revda rivers of Sverdlovsk region, Russia. It was shown that the plants from HMs contaminated habitats characterized by larger sizes of leaves thickness and bigger cells and chloroplasts. Significant changes in elodea sheet thickness and cells dimensions in phenolic polluted area have not been identified. Dimensions of chloroplasts in the impact site decreased. Obviously, this type of resistance to phenol-containing wastewater is due to other security mechanisms. It was shown that chlorophyll content in the Elodea leaves from the polluted water bodies has been increased. Carotenoids content in the impact areas also increased in connection with their antioxidant function, which is particularly evident in stressful conditions.