Surface water sources are increasingly subject to proliferation of toxic cyanobacteria. Direct chlorination of source water containing toxic cyanobacterial cells for different treatment purposes might cause cell damage and toxin release. There is limited information available on chlorination of saxitoxins (STXs: saxitoxin, C-toxins, and gonyautoxins) produced by Anabaena circinalis. This work: (1) investigated the impact of chlorination on cell lysis and toxin/odor compound release in natural waters; (2) assessed the rates of chlorination of total STXs, and (3) estimated apparent rate constants for STX oxidation in ultrapure and natural waters. With a chlorine exposure (CT) value of 7.0 mg x min/L all cells lost viability causing toxin release. Cell-membrane damage occurred faster than released STXs oxidation. All saxitoxin and more than 95% of other STX analogues were subsequently oxidized. Kinetic analysis of the oxidation of STX analogues revealed significant differences in the susceptibility to chlorine, saxitoxin being the easiest to oxidize. Also, concentrations of trihalomethanes, haloacetic acids, and N-nitrosodimethylamine as chlorination byproducts were respectively <50 μg/L and 11 ng/L even at the highest CT value (50.3 mg x min/L).