Harmful algal blooms (HABs) are overgrowths of toxic strains of algae (diatoms, green) and cyanobacteria (blue-green algae). While occurring naturally, human-induced environmental changes have resulted in more frequent occurrences of such blooms worldwide. Meantime, the ecotoxicological risk of HABs is rarely evaluated by means of standard test methods. For the first time, the genotoxic potential of the HAB event 2020 was assessed using two different Tradescantia-based test systems (Trad-SHM and Trad-MN, 24-h exposure). An integrated analysis of biological (algal abundance) and ecotoxicological (testing) data revealed linkages among algal proliferation, changes in Tradescantia stamen hairs (mutations and suppressed growth) and chromosomal aberrations during microsporogenesis (appearance of micronuclei) that were likely to be caused by toxic algal groups. Green alga Botryococcus braunii and the cyanobacterial species Anabaena and Oscillatoria could suppress stamen hair growth; Cyanobacteria Phormidium and Aphanothece sp. could trigger mutations in stamen hairs (appearance of pink and colorless cells); and Oscillatoria sp. could be responsible for the occurrence of chromosomal damage. Diatom proliferation in the spring was not related to the genotoxic response in Tradescantia. Both tests, the Trad-SHM and Trad-MN, are suitable for the evaluation of the toxic potential of HABs.