Microcystins (MCs) are a family of toxic peptides produced by a number of cyanobacteria commonly found in lakes, water reservoirs, and recreational facilities. The increased eutrophication of freshwater supplies has led to an increase in the incidence of cyanobacterial harmful algal blooms and concerns over the public health implications of these toxins in the water supply. Conventional water treatment methods are ineffective at removing low concentrations of cyanotoxins, hence specialized treatment is usually recommended for treatment of contaminated water. In this study, the products of ultrasonically induced degradation of microcystin-LR (MC-LR) and microcystin-RR (MC-RR) were analyzed by LC-MS to elucidate the probable pathways of degradation of these toxins. Results indicate preliminary products of sonolysis of MCs are due to the hydroxyl radical attack on the benzene ring and diene of the Adda peptide residue and cleavage of the Mdha-Ala peptide bond. The effect of pH on the toxin degradation was evaluated since the pH of the solution changes upon ultrasonic irradiation and varies with the water quality of treatable waters. The initial rate of MC-LR degradation is greater at acidic pH and coincides with the change in hydrophobic character of MC-LR as a function of pH. Hydrogen and organic peroxides are formed during ultrasonic irradiation, but can be eliminated by adding Fe(II). The addition of Fe(II) also accelerates the degradation of MC-LR, presumably by promoting the formation of hydroxyl radicals via conversion of ultrasonically produced H2O2. These findings suggest that sonolysis can effectively degrade MCs in drinking water.