An alternating schedule of supply and non-supply adopted in intermittent water distribution systems increases the likelihood of microbial water quality deterioration, as compared to a schedule of continuous supply. Maintaining adequate levels of chlorine in water is the most common remedial strategy adopted to minimize this problem. Thus, it is imperative to understand the kinetics governing the reactions of chlorine with microbial contaminants to optimize the chlorine dosage at the dosing locations. Previous related kinetic studies focused only on controlled experiments with pure microbial cultures in chlorinated water samples. This study addresses uncontrolled contamination caused by sewage intrusion, which is a common problem in developing countries. Uncontrolled contamination is experimentally simulated by adding sewage samples to chlorinated tap water samples. The reaction kinetics is investigated by periodic monitoring of the variability in chlorine and microbial colony counts. A multi-phase kinetic model is found to fit the resulting data. The fit of the model predictions is tested through ANOVA analysis. The proposed model explains the reaction kinetics of chlorine disappearance with less than 5% error. The developed model could be applied to determine optimal chlorine dosages in drinking water distribution systems.