Allelopathic interactions are widespread in all aquatic habitats, among all groups of aquatic primary biomass producers, including cyanobacteria. Cyanobacteria are producers of potent toxins called cyanotoxins, whose biological and ecological roles, including their allelopathic influence, are still incompletely understood. The allelopathic potential of the cyanotoxins microcystin-LR (MC-LR) and cylindrospermopsin (CYL) on green algae (Chlamydomonas asymmetrica, Dunaliella salina, and Scenedesmus obtusiusculus) was established. Time-dependent inhibitory effects on the growth and motility of the green algae exposed to cyanotoxins were detected. Changes in their morphology (cell shape, granulation of the cytoplasm, and loss of flagella) were also observed. The cyanotoxins MC-LR and CYL were found to affect photosynthesis to varying degrees in the green algae Chlamydomonas asymmetrica, Dunaliella salina, and Scenedesmus obtusiusculus, affecting chlorophyll fluorescence parameters such as the maximum photochemical activity (Fv/Fm) of photosystem II (PSII), the non-photochemical quenching of chlorophyll fluorescence (NPQ), and the quantum yield of the unregulated energy dissipation Y(NO) in PSII. In the context of ongoing climate change and the associated expectations of the increased frequency of cyanobacterial blooms and released cyanotoxins, our results demonstrated the possible allelopathic role of cyanotoxins on competing autotrophs in the phytoplankton communities.