Here we report a novel approach to extract, isolate, and characterize high molecular weight organic acids found in the Athabasca oil sands region using preparative capillary gas chromatography (PCGC) followed by thermal conversion/elemental analysis–isotope ratio mass spectrometry (TC/EA-IRMS). A number of different “naphthenic acids” surrogate standards were analyzed as were samples from the bitumen-rich unprocessed McMurray Formation, oil sands process water, groundwater from monitoring wells, and surface water from the Athabasca River. The intramolecular carbon isotope signature generated by online pyrolysis (δ13Cpyr) showed little variation (±0.6‰) within any given sample across a large range of mass fractions separated by PCGC. Oil sand, tailings ponds, and deep McMurray Formation groundwater were significantly heavier (up to ∼9‰) compared to surface water and shallow groundwater samples, demonstrating the potential use of this technique in source apportionment studies.