In this study, a model to optimize residual chlorine concentrations in a water supply system was developed using a multi-objective genetic algorithm. Moreover, to quantify the effects of optimized residual chlorine concentration management and to consider customer service requirements, this study developed indices to quantify the spatial and temporal distributions of residual chlorine concentration. Based on the results, the most economical operational method to manage booster chlorination was derived, which would supply water that satisfies the service level required by consumers, as well as the cost-effectiveness and operation requirements relevant to the service providers. A simulation model was then created based on an actual water supply system (i.e., the Multi-regional Water Supply W in Korea). Simulated optimizations were successful, evidencing that it is possible to meet the residual chlorine concentration demanded by consumers at a low cost.