Abstract Since the 1970s’ disinfection by-products (DBPs) detection, the water treatment specialists’ main focuses were accorded to the DBPs formation, characterization, regulations and control. Involved stages in disinfection process were at a certain level kept at the side as a black box. This paper is a broad review on chlorination applied in water treatment technology especially in terms of involved mechanisms. Chlorine occasions significant injury to bacterial cells, cell permeability dislocation and nucleic acids and enzymes injury. Hypochlorous acid oxidizes sulfhydryl groups, harms iron-sulfur centers, deactivates nutrient transport, hinders cell respiration, and deteriorates the capacity of cells to keep a sufficient adenylate energy charge to stay viable. All disinfectants are highly efficient killing agents. However, these chemical products are very toxic by their selves. Moreover, they interact with NOM, microorganisms, and algae to produce DBPs which are as well poisonous. Consequently, the use of disinfectants must be avoided upon using physical processes or at least reduced as possible at the lowest level.