Water distribution networks (WDNs) could present problems of pathogen intrusion that affect the health of consumers. One solution to diminish this risk is to add more disinfectant to the water at the drinking water treatment plant (DWTP). However, this increases the cost of water treatment and may also cause the formation of trihalomethanes. Mexico has the largest bottled water market in the world. Also, most houses are built with individual storage containers due to intermittent service, which generates a greater residence time of the water before use. This paper shows an alternative to guarantee minimum disinfection along WDNs and diminish the use of disinfectant at the DWTP considering the conditions of water consumption and use in Mexico. We propose a model based on Genetic Algorithms to obtain scenarios where free chlorine is maintained at the minimum permissible concentration throughout the day. In addition, Water Managers could optimize the use of disinfectant by implementing booster chlorination stations (BCSs). The results show that chlorine use could be reduced by 38%, therefore guaranteeing the chlorine concentration limits along the WDN.