Managed aquifer recharge (MAR) systems, such as riverbank filtration, soil aquifer treatment, aquifer storage and recovery, and aquifer storage transfer and recovery, are widely used in drinking water production, water reuse, and subsurface water storage. Potential water sources for MAR (e.g., recycled water, surface water, and stormwater) can contain a wide range of enteric pathogens that pose risks to human health. The long-term operation of full-scale MAR processes confirms significant pathogen reduction. For groundwater recharge with recycled water leading to potable reuse, assigning the log reduction credits for pathogens and microbial indicators is a critical component of the overall design and permitting of advanced water treatment facilities. However, regulators continue to be challenged with assigning appropriate treatment credits for pathogen reduction. This research documented the state of knowledge of pathogen reduction through MAR processes, and assesses the benefits, limitations, and challenges of different regulatory approaches for microbial disease protection. Planners and regulators can rely on this study when considering options for determining defensible pathogen log removal credits in MAR systems. Research partner: California State Water Resources Control Board. Published in 2023.