In this study the effectiveness and feasibility of the degradation of microcystin-LR (MC-LR) using a combined method ozone/Fenton reagent was investigated. The decomposition of the toxin was determined by the chromatographic technique. The effect of the Fenton reaction on the ozonation was observed at various concentrations of ozone at pH 3.0 and 6.8. A low concentration of ozone (0.01 mg/L) given simultaneously with Fenton reagent was more effective in MC-LR degradation than ozone or Fenton reagent treatment individually regardless of the pH. At higher concentrations of ozone the use together with Fenton reagent at pH 6.8 was less efficient in MC-LR degradation than treatment with ozone alone, whereas at pH 3.0 Fenton process turned out to be more effective. The mixture of ozone and hydrogen peroxide was more striking than using ozone with Fenton reagent regardless of the pH. The complete degradation of MC-LR was achieved using ozone alone at a concentration of 0.10 mg/L, whereas the same result using ozonation with Fenton reagent required a dose of ozone of 0.20 mg/L at pH 6.8. In acidic pH the total removal of MC-LR was achieved using ozone alone at a concentration of 0.20 mg/L and the same result was obtained for the combined method of ozone/Fenton reagent.