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Ultra-performance liquid chromatography ion mobility time-of-flight mass spectrometry (UPLC-IM-TOFMS) was utilized for the analysis of naphthenic acids (NAs) in fractions of pH-dependent sequential liquid-liquid extractions from oil sands process-affected water. Ion-mobility separation technique allowed the differentiation of O y S−NAs (2 ≤ y ≤ 4) from O x −NAs (2 ≤ x ≤ 5) via drift time versus retention time separations. The results indicated that the addition of S atom to the O 2 −NA molecule led to a lower increase in the dissociation constant (pK a ) compared to that caused by the addition of O atom. Because additional O is present as OH while the S atom is present as the C S C structure, the latter does not involve into the deprotonation process directly. The pK a value decreased along with increasing carbon number and |Z| number for O 2 −, O 3 −, O 4 −, and O 2 S−NA species, except for O 5 −, O 3 S−, and O 4 S−NA species, each of which are comprised of chemical structures with distinct functional groups. A calculation model was developed to estimate pK a values for individual and total NA species via nonlinear regression curve fitting, utilizing the relative abundances of detected NA species. pK a values were calculated as 3.9 for total NAs, 3.3 for O 2 −NAs, 4.4 for O 3 −NAs, 7.3 for O 4 −NAs, and 4.1 for O 2 S−NAs. Knowledge of NAs pK a is crucially important for the comprehensive understanding of their potential transformation route and toxicity as well as for the development of water remediation applications. Both the ion-mobility separation technique and the new calculation model could be widely applied for the investigation of other complicated pollutants present in water and wastewater. [ABSTRACT FROM AUTHOR]