The oil sands regions of Northern Alberta, Canada, contain an estimated 1.7 trillion barrels of oil in the form of bitumen, representing the second largest deposit of crude oil in the world. A rapidly expanding industry extracts surface‐mined bitumen using alkaline hot water, resulting in large volumes of oil sands process water (OSPW) that must be contained on site due to toxicity. The toxicity has largely been attributed to naphthenic acids (NAs), a complex mixture of naturally occurring aliphatic and (poly‐)alicyclic carboxylic acids. Research has increasingly focused on the environmental fate and remediation of OSPW NAs, but an understanding of these processes necessitates an analytical method that can accurately characterize and quantify NA mixtures. Here we report results of an interlaboratory comparison for the analysis of pure commercial NAs and environmental OSPW NAs using direct injection electrospray ionization mass spectrometry (ESI‐MS) and high‐pressure liquid chromatography/high‐resolution mass spectrometry (HPLC/HRMS). Both methods provided very similar characterization of pure commercial NA mixture; however, the m/z selectivity of HPLC/HRMS was essential to prevent substantial false‐positive detections and misclassifications in OSPW NA mixtures. For a range of concentrations encompassing those found in OSPW (10–100 mg/L), both methods produced linear response, although concentrations of commercial NAs above 50 mg/L resulted in slight non‐linearity by HPLC/HRMS. A three‐fold lower response factor for total OSPW NAs by HPLC/HRMS was largely attributable to other organic compounds in the OSPW, including hydroxylated NAs, which may explain the substantial misclassification by ESI‐MS. For the quantitative analysis of unknown OSPW samples, both methods yielded total NA concentrations that correlated with results from Fourier transform infrared (FTIR), but the coefficients of determination were not high. Quantification by either MS method should therefore be considered semi‐quantitative at best, albeit either method has substantial value in environmental fate experiments where relative concentration changes are the desired endpoints rather than absolute concentrations. Copyright © 2008 John Wiley & Sons, Ltd.