Cooling water deficiency due to limited freshwater sources posed an obstacle of expending current thermoelectric power generation in the U.S. and has led the power industry to seek an alternative water resource to meet its cooling water requirement. Of all the potential alternatives, secondary treated municipal wastewater is prominent because of its vast allocation and abundant quantity. However, the impaired water quality and unique environment make the cooling tower management more challenging. Therefore, prudent water quality management with chemicals is required to prevent corrosion, scaling, and biological growth in the cooling systems. This study focused on the understanding of the kinetic, effectiveness, and dosage requirement of chlorine-based biocides (chlorine, chloramine and chlorine dioxide) in the recirculating cooling systems using treated municipal wastewater as makeup. Laboratory-scale studies and pilot-scale cooling systems were used to evaluate the biological growth under realistic conditions associated with full-scale cooling systems. Results of 30-day field tests indicated that the pilot-scale cooling towers developed in this study are reliable for evaluating different chemical regimes by maintaining steady cooling performance under various operating conditions. Direct use of secondary treated effluent for cooling water is a feasible option when using monochloramine as major biocide. The low oxidizing ability of monochloramine resulted in a high residence time and high penetrating ability, and thus provided better biocidal effectiveness against planktonic and sessile heterotrophic bacteria and Legionella in recirculating cooling systems. A minimum monochloramine residual above 3 mg/L in the recirculating cooling water is needed for proper biological growth control with this impaired water. Biological growth potential is comparable in secondary treated effluent subjected to different tertiary treatment (i.e., nitrification, sand filtration, activated carbon adsorption) regardless of total organic carbon concentration in the wastewater. The performance of monochloramine was optimized when the secondary treated effluent was subjected to nitrification and sand filtration. The key findings of this study indicate that biological growth can be controlled in cooling systems using treated municipal effluents as makeup. The biocide regime demonstrated in this study offers a useful guideline to meet biological growth control criteria in recirculating cooling systems.