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The present study compared the stress response of two microalgal strains – Arthronema africanum (Cyanoprokaryota) and Coelastrella sp. BGV (Chlorophyta), after heavy metals’ treatment. Changes of algal growth, pigment and protein content were analyzed after adding Cu, Cd and Pb (50 µM and 100 µM) to the nutrition medium. It was found that Cd and Pb significantly inhibited growth and protein biosynthesis of microalgae, but the effect of Cu remained less pronounced. In both strains, a decrease of chlorophyll content was observed, while carotenoid content markedly increased, especially in Coelastrella sp. BGV biomass. The addition of 100 µM Cd and 100 µM Pb to the medium caused a strong enhancement of malondialdehyde in both microalgal strains, which corresponded to the significant increase of superoxide dismutase and catalase activity. The antioxidant enzymes appeared to be differently altered by heavy metals’ exposure. The activity of SOD in the Arthronema africanum cells was most strongly affected by Cd, in contrast to Coelastrella sp. BGV that was highly increased by 100 µM Pb. The application of 100 µM Cd and 100 µM Pb increased in a similar manner catalase activity in both microalgae. The strains that were studied showed a high absorption capacity for metal ions, especially for Pb, which was absorbed largely than Cd and Cu. For that reason, we assumed that both microalga and, in particular, Coelastrella sp. BGV, could be successfully used for treatment of contaminated water bodies.