Previous studies on water treatment processes confirmed that preoxidation of the surface water improves the coagulation and filtration processes. However, only few studies focused on its effects on algae and their toxins. In this study, the variability of microcystins through conventional treatment processes was investigated within a full-scale plant, which is challenged with a high level of cyanotoxins and where surface water is pre-chlorinated. Treatment trials were conducted with and without prechlorination. The water characteristics, algal count, and microcystins were compared. The results revealed that, prechlorination causes lysis of Cyanophyta cells, consequently releasing cell bound toxins and other compounds that lead to the formation of harmful disinfection by-products (DBPs). Laboratory jar tests were performed to evaluate potassium permanganate effectiveness as an alternative preoxidant. Unlike prechlorination, permanganate preserved the algal cells integrity, allowing for removal of intact cells with their toxins and provided better controls of DBPs.