Chlorination is an effective method of water disinfection. However, it has been identified as contributing to the formation of a wide variety of disinfection by-products that have been associated with adverse health effects. Natural humic matter and anthropogenic pollutants are responsible for the formation of these by-products. Mass spectrometry is the most efficient tool to analyze the rates of conversion, the nature and levels of by-products in the reactions of chlorinating agents with model organic compounds. More than 30 substrates with various functional groups were studied, while gaseous chlorine and sodium hypochlorite were used as chlorinating agents. The effects of pH, substrate/active chlorine ratio, addition of metal cations and bromides and iodides on the aqueous chlorination process of various organic substrates were investigated. Transformation schemes were proposed for the studied compounds.