Large volumes of oil sands process-affected waters (OSPW) result from heavy oil extraction in Alberta, Canada. Currently, a toxic legacy of ca. 500 Mm3 is stored in tailings ponds under a zero-discharge policy. OSPW is a complex mixture of suspended and dissolved materials including a wide range of inorganic and organic contaminants. Classically defined naphthenic acids (NAs; CnH2n+ZO2) are one of the primary toxic fractions in OSPW and have therefore been the subject of considerable research interest. Most studies employ considerable sample cleanup followed by liquid chromatography and/or high-resolution mass spectrometry (HRMS) for the characterization of these complex mixtures. However, these strategies can be time- and cost-intensive, limiting the scope of research and adoption for regulatory purposes. Condensed phase membrane introduction mass spectrometry (CP-MIMS) is emerging as a “fit-for-purpose” approach for the analysis of NAs. This technique directly interfaces the mass spectrometer with an aqueous sample using a hydrophobic semi-permeable membrane, requiring only pH adjustment to convert NAs to a membrane-permeable form. Here, we examine the perm-selectivity of classical NAs (O2) relative to their more oxidized counterparts (O3–O7) and heteroatomic (N, S) species collectively termed naphthenic acid fraction compounds (NAFCs). The investigation of 14 model compounds revealed that classically defined NAs are greater than 50-fold more membrane permeable than their oxidized/heteroatomic analogs. HRMS analysis of real OSPW extracts with and without membrane clean-up further supported selectivity towards the toxic O2 class of NAs, with >85% of the overall signal intensity attributable to O2 NAs in the membrane permeate despite as little as 34.7 ± 0.6% O2 NAs observed in the directly infused mixture. The information collected with HRMS is leveraged to refine our method for analysis of NAs at unit mass resolution. This new method is applied to 28 archived real-world samples containing NAs/NAFCs from constructed wetlands, OSPW, and environmental monitoring campaigns. Concentrations ranged from 0–25 mg/L O2 NAs and the results measured by CP-MIMS (unit mass) and SPE-HRMS (Orbitrap) showed good agreement (slope = 0.80; R2 = 0.76).