Increasing water scarcity caused by population growth, climate change, pollution from natural and anthropogenic sources, etc. is likely to impact the occurrence of water-associated infectious diseases. Nowadays, access to clean and safe water is a growing concern worldwide. Therefore, disinfection of drinking water is a vital step in public treatment systems as it ensures the removal of various contaminants, including pathogenic microorganisms (protozoa, viruses, bacteria, and intestinal parasites) that give rise to waterborne diseases. Nevertheless, undesirable disinfection byproducts (DBPs) are formed during disinfection as a result of reactions between chemical disinfectants and natural organic matter (NOM), and/or anthropogenic contaminants, and/or bromide/iodide that are present in the raw water. The chemical complexity and heterogeneity of matters in the raw water makes the characterization and the mechanism of DBPs formation quite difficult and ambiguous regardless of the previous hundreds of studies on DBPs generation. As chlorination is still the most economic and most often used disinfection method, and beside chlorination, the application of chlorine dioxide is becoming more widespread, this paper investigates the possible DBPs generated using chlorine and chlorine dioxide with highlighting their adverse health effects. It overviews the reactions of those disinfectants with inorganic and organic compounds. It is important to note that in order to better understand the performance of disinfectants in water treatment, further investigations on the mechanisms of them with inorganic and organic compounds found in water are critically needed.