As the pace of drilling activity in the Marcellus Formation in the northern Appalachian Basin has increased, so has the number of alleged incidents of stray natural gas migration to shallow aquifer systems. For this study, more than 2300 gas and water samples were analyzed for molecular composition and stable isotope compositions of methane and ethane. The samples are from Neogene- to Middle Devonian-age strata in a five-county study area in northeastern Pennsylvania. Samples were collected from the vertical and lateral sections of 234 gas wells during mud gas logging (MGL) programs and 67 private groundwater-supply wells during baseline groundwater-quality testing programs. Evaluation of this geochemical database reveals that microbial, mixed microbial and thermogenic, and thermogenic gases of different thermal maturities occur in some shallow aquifer systems and throughout the stratigraphy above the Marcellus Formation. The gas occurrences predate Marcellus Formation drilling activity. Isotope data reveal that thermogenic gases are predominant in the regional Neogene and Upper Devonian rocks that comprise the potable aquifer system in the upper 305 m (1000 ft) (average delta C-13(1) = -43.53 parts per thousand; average delta C-13(2) = -40.95 parts per thousand; average delta DC1 = -232.50 parts per thousand) and typically are distinct from gases in the Middle Devonian Marcellus Formation (average delta C-13(1) = -32.37 parts per thousand; average delta C-13(2) = 38.48 parts per thousand; average delta C-13(1) = -162.34 parts per thousand). Additionally, isotope geochemistry at the site-specific level reveals a complex thermal and migration history with gas mixtures and partial isotope reversals (delta C-13(1) > delta C-13(2)) in the units overlying the Marcellus Formation. Identifying a source for stray natural gas requires the synthesis of multiple data types at the site-specific level. Molecular and isotope geochemistry provide evidence of gas origin and secondary processes that may have affected the gases during migration. Such data provide focus for investigations where the potential sources for stray gas include multiple, naturally occurring, and anthropogenic gases.