Population growth and climate variability highlight the need to enhance freshwater security and diversify water supplies. Subsurface storage of water in depleted aquifers is increasingly used globally to alleviate disparities in water supply and demand often caused by climate extremes including floods and droughts. Managed aquifer recharge (MAR) stores excess water supplies during wet periods via infiltration into shallow underlying aquifers or direct injection into deep aquifers for recovery during dry seasons. Additionally, MAR can be designed to improve recharge water quality, particularly in the case of soil aquifer treatment and riverbank filtration. While there are many potential benefits to MAR, introduction of recharge water can alter the native geochemical and hydrological conditions in the receiving aquifer, potentially mobilizing toxic, naturally occurring (geogenic) contaminants from sediments into groundwater where they pose a much larger threat to human and ecosystem health. On the basis of the present literature, arsenic poses the most widespread challenge at MAR sites due to its ubiquity in subsurface sediments and toxicity at trace concentrations. Other geogenic contaminants of concern include fluoride, molybdenum, manganese, and iron. Water quality degradation threatens the viability of some MAR projects with several sites abandoning operations due to arsenic or other contaminant mobilization. Here, we provide a critical review of studies that have uncovered the geochemical and hydrological mechanisms controlling mobilization of arsenic and other geogenic contaminants at MAR sites worldwide, including both infiltration and injection sites. These mechanisms were evaluated based on site-specific characteristics, including hydrological setting, native aquifer geochemistry, and operational site parameters (e.g., source of recharge water and recharge/recovery cycling). Observed mechanisms of geogenic contaminant mobilization during MAR via injection include shifting redox conditions and, to a lesser extent, pH-promoted desorption, mineral solubility, and competitive ligand exchange. The relative importance of these mechanisms depends on various site-specific, operational parameters, including pretreatment of injection water and duration of injection, storage, and recovery phases. This critical review synthesizes findings across case studies in various geochemical, hydrological, and operational settings to better understand controls on arsenic and other geogenic contaminant mobilization and inform the planning and design of future MAR projects to protect groundwater quality. This critical review concludes with an evaluation of proposed management strategies for geogenic contaminants and identification of knowledge gaps regarding fate and transport of geogenic contaminants during MAR.