One of the most common pollutants in natural ecosystems is heavy metals. Algae are sensitive to the action of heavy metals. This allows to use algae to assess the toxicity of heavy metals, bioindication, and during phycoremediation. This study examines the effect of different Zn and Mn concentrations (1.0, 5.0, 25.0, 50.0, 500.0, 1000.0 mg L-1) on green algae Bracteacoccus minor and Lobosphaera incisa in a chronic bioassay. The results of this study showed that the toxic effect of Zn and Mn on B. minor and L. incisa begins to manifest itself at the lowest of the studied metal concentrations-1 mg L-1. The critical concentration of Zn, which leads to the complete death of B. minor and L. incisa, is 50.0 and 500.0 mg L-1, and Mn is 1000.0 mg L-1 and 500.0 mg L-1, respectively. It was found that principal component (PC) 1 accounts for 60.47% of the total variance and reflects changes associated with low concentrations of heavy metals (up to 5.0 mg L-1). PC2 accounts for 27.95% of the total variance. PC2 is mostly associated with high concentrations of ions of heavy metals. Thus, the effect of Zn and Mn concentrations up to 5 mg L-1and above 50 mg L-1on B. minor and L. incisa has a different character. At the same time, the response of the studied algae species to the action of Zn and Mn has individual differences. In general, B. minor is more resistant to Mn, while L. incisa is more resistant to Zn.