Objective To introduce synergetic inactivation of microorganisms in drinking water by short-term free chlorination for less than 15 minutes followed by monochloramination. Methods Indicator microorganisms such as Escherichia coli, Staphylococcus aureus, Candida albicans, and spores of Bacillus subtilis were used to assess the efficiency of sequential chlorination and free chlorination. Results The sequential chlorination was more efficient in inactivating these microorganisms than free chlorination, indicating that synergy was provided by free chlorine and monochloramine. Ammonia addition time, temperature and pH had influences on this synergy. Conclusion The possible mechanism of this synergy might involve three aspects: free chlorine causing sublethal injury to microorganisms and monochloramine further inactivating them; different ability of free chlorine and monochloramine to penetrate and inactivate microorganism congeries; and higher concentration of residual chlorine in sequential chlorination than in free chlorination. Objective To introduce synergetic inactivation of microorganisms in drinking water by short-term free chlorination for less than 15 minutes followed by monochloramination. Methods Indicator microorganisms such as Escherichia coli, Staphylococcus aureus, Candida albicans, and spores of Bacillus subtilis were used to assess the efficiency Results of the sequential chlorination was more efficient in inactivating these microorganisms than free chlorination, indicating that synergy was provided by free chlorine and monochloramine. Ammonia addition time, temperature and pH had influences on this synergy. Conclusion The possible mechanism of this synergy might involve three aspects: free chlorine causing sublethal injury to microorganisms and monochloramine further inactivating them; different ability of free chlorine and monochloramine to penetrate and inactivate microorganism congeries; and higher concentration of residual chlorine in sequentia l chlorination than in free chlorination.