A rapidly expanding oil sands industry in Canada produces and indefinitely stores large volumes of toxic aqueous tailings containing high concentrations of naphthenic acids (NAs), a complex mixture of naturally occurring aliphatic or alicyclic carboxylic acids. Although there is an acknowledged need to reduce the environmental risks posed by NAs, little is understood about their environmental fate due to a lack of appropriate analytical methods. A dilute-and-shoot reversed-phase capillary HPLC/QTOF-MS method was developed that combines high specificity and sensitivity, quantitative capabilities, the ability to detect novel transformation products, and new structural information within each NA isomer class. HPLC separated NAs, based on carbon number, degree of cyclization, and the extent of alkyl branching, and in so doing increased analytical sensitivity up to 350-fold while providing additional specificity compared to infusion techniques. For tailings water, an interlaboratory study revealed many differences in isomer class profiles compared to an established GC/MS method, much of which was attributed to the misclassification of oxidized NAs (i.e., NA + O) by low-resolution GC/MS. HPLC/QTOF-MS enabled the detection of oxidized products in the same chromatographic run, and Van Krevelen diagrams were adapted to visualize the complex data. A marked decrease of retention times was evident in Syncrude tailings water compared to a commercial mixture, suggesting that tailings water is dominated by highly persistent alkyl-substituted isomers. A biodegradation study revealed that tailings water microorganisms preferentially deplete the least alkyl-substituted fraction and may be responsible for the NA profile in aged tailings water.