Water quality degradation by decommissioned mining sites is an environmental issue recognized globally. In the Ore mountains of Central Europe, a wide array of contaminants is released by abandoned under- and aboveground mining sites threatening the quantity and quality of surface and groundwater resources. Here, we focus on the less-explored internal pollution processes within these mines involving organic carbon and microorganisms in trace metal(loid)s mobilization processes. Over an 18-month period, we conducted hydrological and biogeochemical monitoring at the Reiche Zeche mine, a former lead-zinc-silver mine, in Germany, reaching 230 meters below ground, well below the critical zone. Our results show strong seasonal fluctuations in water availability, concentrations of metal(loid)s, pH, and dissolved organic matter (DOM) components across multiple depths. Excess metal(loid) presence during high flow conditions indicated mobilization behavior deviating from conservative dilution. Our findings reveal strong positive correlations between metal(loid) variability and pH (0.894), and between metal(loid) variability and the DOM fluorescent component C2 (-0.910), a proxy for microbial activity. Accordingly, the microbial processes may significantly contribute to the observed metal(loid) composition and fluxes. By elucidating the intricate roles of hydrological and biogeochemical factors in trace metal(loid) mobilization, our research offers a comprehensive framework for improving mine water management and remediation, potentially informing global environmental policies and sustainable mining practices.