The aim of our study was to investigate the intracellular toxicity mechanisms of the photoactive, potentially anti-cyanobacterial agent hydrogen peroxide (H2O2) in Microcystis aeruginosa, which represents one of the most significant toxin-producing cyanobacterial species in European water bodies. Metabolic activity and cell membrane integrity were evaluated by flow cytometry in cyanobacteria exposed to H2O2 in the dark or light; the relationships between exposure effects and the kinetics of hydrogen peroxide decomposition were studied. In the light (irradiance 140 µmol m−2 s−1), cyanobacteria were exposed to initial H2O2 concentrations of 0.00 (control), 0.75, 2.00, and 4.00 mg l−1 respectively, while in the dark concentrations were ten times higher. Flow cytometry and chlorophyll a fluorescence measurements suggested that hydrogen peroxide exposure elicits an immediate decline of metabolic (esterase) activity, measured as a decrease in fluorescein fluorescence after hydrolysis of fluorescein diacetate (FDA), and immediate changes of chlorophyll a fluorescence parameters, followed later by an increase in the percentage of membrane-compromised (SYTOX Green positive) cells. When the concentration of H2O2 used was lethal (in the two highly exposed treatments in the light), a significant drop in total cell counts was detected, whereas in other treatments no drop was observed during the entire experimental period (72 h). Our study also confirmed that light is one of the critical factors affecting H2O2 decomposition and thus greatly influences its toxicity. Whereas in the light, M. aeruginosa exposed to 0.75 mg l−1 H2O2 recovered after all the H2O2 had decomposed, in the dark H2O2 decomposed relatively slowly and its toxic effects on the cyanobacteria were observed over the whole 72-h period, though without cell lysis in any experimental concentration.