Toxin-producing cyanobacteria are abundant in surface waters used as drinking water resources. Microcystins (MC) produced by certain cyanobacteria present acute and chronic toxicity, and their removal in drinking water treatment processes is of increasing concern. Previous studies have demonstrated that chlorine and potassium permanganate are feasible oxidants for the removal of MCs present in drinking water resources, although the oxidation might lead to toxic oxidation products. In this paper, the toxicity of the oxidation products of MC-LR and -RR has been studied using protein phosphatase 1 inhibition assay (PPIA). The HPLC and ELISA analyses correlated with the PPIA results for both toxins. The samples containing the oxidation products were fractionated by HPLC and the toxicity of the fractions was tested with PPIA. The results revealed that protein phosphatase 1 inhibition emerged only from intact MC, while the oxidation products were non-toxic. Similar results were obtained in experiments performed in natural waters: no reaction products or interactions exhibiting protein phosphatase 1 inhibition were detected.