Exploration of unconventional natural gas reservoirs such as impermeable shale basins through the use of horizontal drilling and hydraulic fracturing has changed the energy landscape in the USA providing a vast new energy source. The accelerated production of natural gas has triggered a debate concerning the safety and possible environmental impacts of these operations. This study investigates one of the critical aspects of the environmental effects; the possible degradation of water quality in shallow aquifers overlying producing shale formations. The geochemistry of domestic groundwater wells was investigated in aquifers overlying the Fayetteville Shale in north-central Arkansas, where approximately 4000 wells have been drilled since 2004 to extract unconventional natural gas. Monitoring was performed on 127 drinking water wells and the geochemistry of major ions, trace metals, CH4 gas content and its C isotopes (δ13CCH4), and select isotope tracers (δ11B, 87Sr/86Sr, δ2H, δ18O, δ13CDIC) compared to the composition of flowback-water samples directly from Fayetteville Shale gas wells. Dissolved CH4 was detected in 63% of the drinking-water wells (32 of 51 samples), but only six wells exceeded concentrations of 0.5 mg CH4/L. The δ13CCH4 of dissolved CH4 ranged from −42.3‰ to −74.7‰, with the most negative values characteristic of a biogenic source also associated with the highest observed CH4 concentrations, with a possible minor contribution of trace amounts of thermogenic CH4. The majority of these values are distinct from the reported thermogenic composition of the Fayetteville Shale gas (δ13CCH4 = −35.4‰ to −41.9‰). Based on major element chemistry, four shallow groundwater types were identified: (1) low (<100 mg/L) total dissolved solids (TDS), (2) TDS > 100 mg/L and Ca–HCO3 dominated, (3) TDS > 100 mg/L and Na–HCO3dominated, and (4) slightly saline groundwater with TDS > 100 mg/L and Cl > 20 mg/L with elevated Br/Cl ratios (>0.001). The Sr (87Sr/86Sr = 0.7097–0.7166), C (δ13CDIC = −21.3‰ to −4.7‰), and B (δ11B = 3.9–32.9‰) isotopes clearly reflect water–rock interactions within the aquifer rocks, while the stable O and H isotopic composition mimics the local meteoric water composition. Overall, there was a geochemical gradient from low-mineralized recharge water to more evolved Ca–HCO3, and higher-mineralized Na–HCO3 composition generated by a combination of carbonate dissolution, silicate weathering, and reverse base-exchange reactions. The chemical and isotopic compositions of the bulk shallow groundwater samples were distinct from the Na–Cl type Fayetteville flowback/produced waters (TDS ∼10,000–20,000 mg/L). Yet, the high Br/Cl variations in a small subset of saline shallow groundwater suggest that they were derived from dilution of saline water similar to the brine in the Fayetteville Shale. Nonetheless, no spatial relationship was found between CH4 and salinity occurrences in shallow drinking water wells with proximity to shale-gas drilling sites. The integration of multiple geochemical and isotopic proxies shows no direct evidence of contamination in shallow drinking-water aquifers associated with natural gas extraction from the Fayetteville Shale.