In disinfection systems, incomplete penetration of chlorine into effluent wastewater particles can result in a residual population of viable microorganisms. In this work, a combined experimental and numerical approach was used to quantify inactivation of microorganisms in effluent particles and identify combinations of particle removal and chlorine dose that would result in a reduction of occluded microorganisms for six full-scale facilities in the United States with different nitrification levels. The results reveal that combined chlorine is more effective for inactivating occluded microorganisms than free chlorine; model calibration results suggest that free chlorine is less effective because it is more reactive. However, nitrified effluents appear to have lower effluent particle concentrations, and decreases in particle concentrations significantly reduce the chlorine required. Additionally, in disinfection systems that are designed and operated based on inactivation of indicator organisms, the chlorine dose may be insufficient to inactivate occluded pathogens to levels consistent with current regulations.