Manganese (Mn) contamination of well water is recognized as an environmental health concern. In the southeastern Piedmont region of the United States, well water Mn concentrations can be >2 orders of magnitude above health limits, but the specific sources and causes of elevated Mn in groundwater are generally unknown. Here, using field, laboratory, spectroscopic, and geospatial analyses, we propose that natural pedogenetic and hydrogeochemical processes couple to export Mn from the near-surface to fractured-bedrock aquifers within the Piedmont. Dissolved Mn concentrations are greatest just below the water table and decrease with depth. Solid-phase concentration, chemical extraction, and X-ray absorption spectroscopy data show that secondary Mn oxides accumulate near the water table within the chemically weathering saprolite, whereas less-reactive, primary Mn-bearing minerals dominate Mn speciation within the physically weathered transition zone and bedrock. Mass-balance calculations indicate soil weathering has depleted over 40% of the original solid-phase Mn from the near-surface, and hydrologic gradients provide a driving force for downward delivery of Mn. Overall, we estimate that >1 million people in the southeastern Piedmont consume well water containing Mn at concentrations exceeding recommended standards, and collectively, these results suggest that integrated soil-bedrock-system analyses are needed to predict and manage Mn in drinking-water wells.