Microcystin-LR (MC-LR), a toxin produced by cyanobacteria, is very toxic and poses a threat to public health when entering water treatment works. In this study, UV/chlorine process, as an advanced oxidation process (AOP), has been demonstrated for effective elimination of MC-LR levels and associated toxicity. At a chlorine dose of 3.0 mg L−1 and UV fluence of 125 mJ cm−2, MC-LR (initial concentration 1.0 μM) was reduced by 92.5%, which was much higher than 20.3% removal under UV irradiation alone and 65.1% removal during dark chlorination. Enhanced degradation was attributed by hydroxyl radicals (HO) and reactive chlorine species (RCS), mainly Cl2- and ClO. Increasing chlorine doses or lowering pH favored MC-LR removal. Increased bicarbonate and natural organic matter concentrations inhibited MC-LR removal, but bromide ions enhanced MC-LR removal instead. MC-LR elimination rates in natural waters were roughly two times smaller than those in ultrapure water. The reactive radicals promoted hydroxylation of both diene of Adda moiety and double bond of Mdha moiety in MC-LR. UV exposure enhanced the dechlorination of chloro-MC-LR via the cleavage of CCl bond. The toxicity was evaluated by a protein phosphatase (PP2A) inhibition assay. At a chlorine dose of 3.0 mg L−1 and UV fluence of 125 mJ cm−2, the toxicity of the treated water was reduced by 75.0%, which was also higher than 25.7% and 46.7% removal under UV irradiation alone and during dark chlorination, respectively. These results highlight UV/chlorine is an efficient AOP for MC-LR degradation and detoxification. Display omitted •UV254 irradiation combined with chlorine exhibits synergic effects on MC-LR degradation.•MC-LR degradation rate was inhibited by NOM and HCO3−; but accelerated by Br−.•MC-LR degradation mechanisms and products were proposed.•Reactive radicals (HO.•, Cl2•-, and ClO•) contributed to MC-LR degradation.