Multi-layer commingling coalbed methane (CBM) development causes interlayer interference, which can severely impede the efficient pressure drop in CBM reservoirs and make it difficult to identify the produced water source. In this study, geochemical analyses (conventional ions, stable isotopes, and trace elements) were conducted on 38 water samples collected from 11 CBM wells, an adjacent river and the coal mine in the Bide-Santang Basin, western Guizhou, China. Variations in water quality caused by aquifer recharge, water-rock interactions, and the oxidation environment were revealed using principle component analysis and hierarchical cluster analysis. Li, Ga, Rb, Sr, and Ba were selected as characteristic trace elements, whose concentrations tend to increase with increasing producing layer depth. The water samples recorded an obvious D drift trend relative to the local meteoric water line (LMWL). Fracturing fluid from contaminated wells recorded elevated Cl− and Na+ concentrations and high δ18O and δD values. The geochemical parameters of d (the degree of D drift), δD, δ18O, Cl− + Na+ and characteristic trace element concentrations in produced water serve as indicators of the production and water source of CBM wells. Templates were created to discriminate between sources of produced water, including shallow groundwater, coal seam water, and fracturing fluid water. High-production wells are characterized by producing coal seam water, while low-production wells are characterized by producing shallow groundwater. The upper CBM system is susceptible to shallow groundwater recharge that involves multiple limestone aquifers, so it is recommended that the middle and lower CBM systems should be a priority for CBM development.