The mobility of molybdenum (Mo) in groundwater systems has received little attention, although a high intake of Mo is known to be detrimental to human and animal health. Here, we used a comprehensive hydrochemical data set collected during a multi-cycle aquifer storage and recovery test to study the mechanisms that control the mobility of Mo under spatially and temporally varying hydrochemical conditions. The model-based interpretation of the data indicated that the initial mobilization of Mo occurs as a sequence of reactions, in which (i) the aerobic injectant induces pyrite oxidation, (ii) the released acidity is partially buffered by the dissolution of dolomite that (iii) leads to the release of Mo with highly soluble sulfurized organic matter prevailing between the intercrystalline spaces of the dolomite matrix or incorporated in dolomite crystals. Once released, Mo mobility was primarily controlled by pH-dependent surface complexation reactions to the sediments and, to a lesser extent, the capture by iron sulfides (FeS). In the studied system, Mo mobilization could be effectively mitigated by reducing or eliminating pyrite oxidation, which decreases the likelihood of dolomite dissolution and associated Mo release.