Chemical kinetics were determined for the reactions of ozone and hydroxyl radicals with the three cyanotoxins microcystin-LR (MC-LR), cylindrospermopsin (CYN) and anatoxin-a (ANTX). The second-order rate constants (kO3) at pH 8 were 4.1 ± 0.1 × 105 M-1 s-1 for MC-LR, ∼3.4 × 105 M-1 s-1 for CYN, and ∼6.4 × 104 M-1 s-1 for ANTX. The reaction of ozone with MC-LR exhibits a kO3 similar to that of the conjugated diene in sorbic acid (9.6 ± 0.3 × 105 M-1 s-1) at pH 8. The pH dependence and value of k O3 for CYN at pH > 8 (∼2.5 ± 0.1 × 106 M-1 s-1) are similar to deprotonated amines of 6-methyluracil. The kO3 of ANTX at pH > 9 (∼8.7 ± 2.2 × 105 M-1 s-1) agrees with that of neutral diethylamine, and the value at pH < 8 (2.8 ± 0.2 × 104 M-1 s-1) corresponds to an olefin. Second-order rate constants for reaction with OH radicals (•OH), kOH for cyanotoxins were measured at pH 7 to be 1.1 ± 0.01 × 1010 M-1 s-1 for MC-LR, 5.5 ± 0.01 × 109 M-1 s-1 for CYN, and 3.0 ± 0.02 × 109 M-1 s-1 for ANTX. Natural waters from Switzerland and Finland were examined for the influence of variations of dissolved organic matter, SUVA254, and alkalinity on cyanotoxin oxidation. For a Swiss water (1.6 mg/L DOC), 0.2, 0.4, and 0.8 mg/L ozone doses were required for 95% oxidation of MC-LR, CYN, and ANTX, respectively. For the Finnish water (13.1 mg/L DOC), >2 mg/L ozone dose was required for each toxin. The contribution of hydroxyl radicals to toxin oxidation during ozonation of natural water was greatest for ANTX > CYN > MC-LR. Overall, the order of reactivity of cyanotoxins during ozonation of natural waters corresponds to the relative magnitudes of the second-order rate constants for their reaction with ozone and •OH. Ozone primarily attacks the structural moieties responsible for the toxic effects of MC-LR, CYN, and ANTX, suggesting that ozone selectively detoxifies these cyanotoxins.