Molybdenum (Mo) is an essential trace nutrient but has negative health effects at high concentrations. Groundwater typically has low Mo (<2 μg/L), and elevated levels are associated with anthropogenic contamination, although geogenic sources have also been reported. Coal combustion residues (CCRs) are enriched in Mo, and thus present a potential anthropogenic contamination source. Here, we use diagnostic geochemical tracers combined with groundwater residence time indicators to investigate the sources of Mo in drinking-water wells from shallow aquifers in a region of widespread CCR disposal in southeastern Wisconsin. Samples from drinking-water wells were collected in areas near and away from known CCR disposal sites, and analyzed for Mo and inorganic geochemistry indicators, including boron and strontium isotope ratios, along with groundwater tritium-helium and radiogenic 4He in-growth age-dating techniques. Mo concentrations ranged from <1 to 149 μg/L. Concentrations exceeding the U.S. Environmental Protection Agency health advisory of 40 μg/L were found in deeper, older groundwater (mean residence time >300 y). The B (δ11B = 22.9 ± 3.5‰) and Sr (87Sr/86Sr = 0.70923 ± 0.00024) isotope ratios were not consistent with the expected isotope fingerprints of CCRs, but rather mimic the compositions of local lithologies. The isotope signatures combined with mean groundwater residence times of more than 300 years for groundwater with high Mo concentrations support a geogenic source of Mo to the groundwater, rather than CCR-induced contamination. This study demonstrates the utility of a multi-isotope approach to distinguish between fossil fuel-related and natural sources of groundwater contamination.