The growth of human population leads to intensification of agriculture and promotes, through eutrophication, development of cyanobacteria. One of the most widespread and bloom-forming species in freshwater is toxic Microcystis aeruginosa (M. aeruginosa). Combustion of fossil fuels and metallurgical processes are the main sources of heavy metals contamination in surface water including cadmium (Cd) and lead (Pb). The following study was conducted in order to determine the effect of 1–20 mg·L^-1 of Cd and Pb on photochemistry (using flow cytometry) and growth (based on chlorophyll concentration) of M. aeruginosa as well as to estimate levels of metal bioaccumulation. We have found that 1–10 mg·L^-1 of Cd and 1–5 mg·L^-1 of Pb induced continuous enhancement of chlorophyll fluorescence during 24 h of incubation. No significant degradation of chlorophyll was observed in these samples. At higher concentrations of 20 mg·L^-1 of Cd and 10–20 mg·L^-1 of Pb chlorophyll level significantly decreased and its fluorescence was quenched. M. aeruginosa demonstrated high capability of Cd and Pb bioaccumulation, proportionally to initial metal concentration. In samples with initial concentration of 20 mg·L^-1 of Cd and Pb bioaccumulation of 87.3% and 90.1% was observed, respectively. Our study demonstrates that M. aeruginosa can potentially survive in highly metals polluted environments, be a primary source of toxic metals in the food chain and consequently contribute to enhanced toxicity of heavy metals to living organisms including human.