Seasonal algal blooms in surface waters can impact water quality through an input of algal organic matter (AOM) to the pool of dissolved organic matter as well as the release of cyanotoxins. The formation and speciation of disinfection byproducts (DBPs) during chlorination of algal-impacted waters, collected from growth of Microcystis aeruginosa were studied. Second-order rate constants for the reactions of microcystins (MCs) with chlorine and bromine were determined. Finally, the toxicity of chlorinated algal-impacted waters was evaluated by Chinese hamster ovary (CHO) cytotoxicity and genotoxicity assays. Under practical water treatment conditions, algal-impacted waters produced less regulated trihalomethanes (THMs) and haloacetic acids (HAAs), haloacetonitriles (HANs), and total organic halogen (TOX) than natural organic matter (NOM). For example, the weight ratios of DBP formation from AOM to NOM (median levels) were approximately 1:5, 1:3, 1:2 and 1:3 for THMs, HAAs, HANs, and TOX, respectively. Increasing initial bromide level significantly enhanced THM and HAN concentrations, and therefore unknown TOX decreased. The second-order rate constant for the reactions of MC-LR (the most common MC species) with chlorine was 60 M⁻¹ s⁻¹ at pH 7.5 and 21 °C, and the rate constants for MC congeners follow the order: MC-WR > MC-LW > MC-YR > MC-LY > MC-LR ≈ MC-RR. The reaction rate constant of bromine with MC-LR is two orders of magnitude higher than that of chlorine. Unchlorinated algal-impacted waters were toxic owning to the presence of MCs, and chlorination enhanced their cytotoxicity and genotoxicity due to the formation of toxic halogenated DBPs. However, the toxicity of treated waters depended on the evolution of cyanotoxins and formation of DBPs (particularly unknown or emerging DBPs).