The effect of permanganate oxidation was investigated as water treatment strategy with a focus on comparing the reaction characteristics of NaOCl and sodium permanganate (NaMnO4) in algae (Monoraphidium sp., Micractinium inermum, Microcystis aeruginosa)-contained water. Flow cytometry explained that chlorine exposure easily damaged algae cells. Damaged algae cells release intracellular organic matter, which increases the concentration of organic matter in the water, which is higher than by NaMnO4. The oxidation reaction resulted in the release of toxin (microcystin-LR, MC-LR) in water, and the reaction of algal organic matter with NaOCl resulted in trihalomethanes (THMs) concentration increase. The oxidation results by NaMnO4 significantly improved the concentration reduction of THMs and MC-LR. Therefore, this study suggests that NaMnO4 is effective as a pre-oxidant for reducing algae damage and byproducts in water treatment process.