Managed aquifer recharge (MAR) is an increasingly used water management technique that enhances water availability while commonly generating water quality benefits. However, MAR activities may also trigger adverse geochemical reactions, especially during the injection of oxidant-enriched waters into reducing aquifers. Where this occurs, the environmental risks and the viability of mitigating them must be well understood. Here, we develop a rigorous approach for assessing and managing the risks from MAR-induced metal mobilization. First, we develop a process-based reactive transport model to identify and quantify the main hydrogeochemical drivers that control the release of metals and their mobility. We then apply a probabilistic framework to interrogate the inherent uncertainty associated with adjustable model parameters and consider this uncertainty (i) in long-term predictions of groundwater quality changes and (ii) in scenarios that investigate the effectiveness of modifications in the water treatment process to mitigate metal release and mobility. The results suggested that Co, Ni, Zn, and Mn were comobilized during pyrite oxidation and that metal mobility was controlled (i) by the sediment pH buffering capacity and (ii) by the sorption capacity of the native aquifer sediments. Both tested mitigation strategies were shown to be effective at reducing the risk of elevated metal concentrations.