Freshwater cyanobacterial blooms are becoming increasingly problematic microbiological pollutants, especially for the water resource and surface natural lakes. Cyanobacterial blooms, which produce toxins and microcystins, negatively affect the quality of water, animal, and human health, and they have also negative impact on recreational activities. The effect of electrochemically prepared potassium ferrate (green oxidation agent) on the water polluted by cyanobacteria and cyanotoxins was studied. The two most frequently occurring cyanobacterial genus Microcystis and Anabaena and the most toxic and abundant microcystin MC-LR were successfully inactivated and treated by ferrate. Potassium ferrates were applied at different conditions, such as varied hydrodynamics flow of samples, pH, and Fe(VI) concentrations. High detected elimination efficiency was consequently tested on the real water matrix from microbiological polluted natural lake Šaštín-Gazárka in Slovakia. The ferrate application leads to the better chemical, biological, microbiological, and ecotoxicological outcomes.