Managed aquifer recharge (MAR) is used worldwide in urban environments to replenish groundwater to provide a secure and sustainable supply of potable and non-potable water. It relies on natural treatment processes within aquifers (i.e., filtration, sorption, and degradation), and in some cases involves infiltration through the unsaturated zone to polish the given source water, e.g., treated wastewater, stormwater, or rainwater, to the desired quality prior to reuse. Whilst MAR in its early forms has occurred for millennia, large-scale schemes to replenish groundwater with advanced treated reclaimed water have come to the fore in cities such as Perth, Western Australia, Monterey, California, and Changwon, South Korea, as water managers consider provision for projected population growth in a drying climate. An additional bonus for implementing MAR in coastal aquifers is assisting in the prevention of seawater intrusion. This review begins with the rationale for large-scale MAR schemes in an Australian urban context, reflecting on the current status; describes the unique benefits of several common MAR types; and provides examples from around the world. It then explores several scientific challenges, ranging from quantifying aquifer removal for various groundwater contaminants to assessing risks to human health and the environment, and avoiding adverse outcomes from biogeochemical changes induced by aquifer storage. Scientific developments in the areas of water quality assessments, which include molecular detection methods for microbial pathogens and high resolution analytical chemistry methods for detecting trace chemicals, give unprecedented insight into the "polishing" offered by natural treatment. This provides opportunities for setting of compliance targets for mitigating risks to human health and maintaining high performance MAR schemes.