The high levels of acid extractable organics (AEOs) containing naphthenic acids (NAs) found in oil sands process-affected waters (OSPW) are a growing concern in monitoring studies of aquatic ecosystems in the Athabasca oil sands region. The complexity of these compounds has substantially hindered their accurate analysis and quantification. Using a recently developed technique which determines the intramolecular carbon isotope signature of AEOs generated by online pyrolysis (δ13Cpyr), natural abundance radiocarbon, and high resolution Orbitrap mass spectrometry analyses, we evaluated the sources of AEOs along a groundwater flow path from a major oil sands tailings pond to the Athabasca River. OSPW was characterized by a δ13Cpyr value of approximately −21‰ and relatively high proportions of O2 and O2S species classes. In contrast, AEO samples located furthest down-gradient from the tailings pond and from the Athabasca River were characterized by a δ13Cpyr value of around −29‰, a greater proportion of highly oxygenated and N-containing compound classes, and a significant component of nonfossil and, hence, non-bitumen-derived carbon. The groundwater concentrations of mining-related AEOs determined using a two end-member isotopic mass balance were between 1.6 and 9.3 mg/L lower than total AEO concentrations, implying that a less discriminating approach to quantification would have overestimated subsurface levels of OSPW. This research highlights the need for accurate characterization of “naphthenic acids” in order to quantify potential seepage from tailings ponds.