With the increasing environmental impacts of human activities, the problem of polygenic multipollutants in groundwater has attracted the attention of researchers. Identifying the hydrobiogeochemical characteristics of the surface sewage that replenishes groundwater is crucial to addressing this problem. The input of polygenic multipollutants into groundwater leads to not only the mechanical superposition of pollutants but also the formation of secondary pollutant types. The evolution of polygenic multipollutants is influenced by aquifer characteristics, carbon sources, microbial abundance, etc. Therefore, this study took a sewage leakage point in Northwest China as the research object, carried out a controlled laboratory experiment on the impact of sewage discharge on groundwater, and, combined with long-term field monitoring results, determined the main hydrobiogeochemical processes of polygenic multipollutants and their secondary pollutants. The results showed that the redox environment and the gradient change in pH were identified as the most critical controlling factors. In oxidative groundwater during the early stage of vertical infiltration, sewage carries a substantial amount of NH
4+, which is oxidized to form the secondary pollutant NO
3−. As O
2 is consumed, the reduction intensifies, and secondary pollutants NO
3−, Mn (IV), and Fe(III) minerals are successively reduced. Compared with the natural conditions of rainwater vertical infiltration, the reaction rates and intensities of various reactions significantly increase during sewage vertical infiltration. However, there is a notable difference in the groundwater pH between sewage and rainwater vertical infiltration. In O
2 and secondary pollutant NO
3− reduction, a large amount of CO
2 is rapidly generated. Excessive CO
2 dissolves to produce a substantial amount of H
+, promoting the acidic dissolution of Mn (II) minerals and generation of Mn
2+. Sewage provides a higher carbon load, enhancing Mn (II) acidic dissolution and stimulating the activity of dissimilatory nitrate reduction to ammonium, which exhibits a higher contribution to NO
3− reduction. This results in a portion of NO
3− converted from NH
4+ being reduced back to NH
4+ and retained in the groundwater, reducing the denitrification’s capacity to remove secondary NO
3−. This has important implications for pollution management and groundwater remediation, particularly monitored natural attenuation.
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