The potential risk of multiple contaminants mobilization from sediment was evaluated under the infiltration of reactive organic matter (OM) during groundwater recharge. Significant NH4-N, PO43−, As, Fe, and Mn release were observed which show elevated peaks in the initial stage (0–19 d) and declines afterwards until reach quite low and stable content (20–37 d). When re-oxidize with SO42− (38–65 d), the reducing condition is stimulated to release more Fe and Mn however no As, NH4-N and PO43−. The microbial reductive Fe oxides dissolution is the main driving force for NH4-N, PO43−, As, Fe, and Mn release. The NH4-N and PO43− release was attributed by passive mobilization from Fe/Mn oxides due to its dissolution. The cation exchange also works significantly on NH4+ release while desorption works on PO43− as well. Microorganism responses to the infiltration reactive OM and further impacts the mobilization of multiple contaminants. The precipitation of secondary Fe/Mn minerals accompanied by co-precipitation and/or re-absorption lower down their aqueous levels. However, this aqueous contamination risk was hidden in solid reactive secondary minerals when oxidizer like SO42− perturbs the recurrence of Fe and Mn contamination occurs. This shows the perennial release of nutrients and trace elements should be paid attention in areas with reactive OM infiltration followed by redox/groundwater chemistry fluctuations, potentially in hyporheic zone of river/lake, managed aquifer recharge zone, etc.