The extraction of bitumen from the oil sands in Canada releases toxic naphthenic acids into the process-affected waters. The development of an ideal analytical method for quantifying naphthenic acids (general formula CnH2n + ZO2) has been impeded by the complexity of these mixtures and the challenges of differentiating naphthenic acids from other naturally-occurring organic acids. The oil sands industry standard FTIR method was compared with a newly-developed GC–MS method. Naphthenic acids concentrations were measured in extracts of surface and ground waters from locations within the vicinity of and away from the oil sands deposits and in extracts of process-affected waters. In all but one case, FTIR measurements of naphthenic acids concentrations were greater than those determined by GC–MS. The detection limit of the GC–MS method was 0.01 mg L−1 compared to 1 mg L−1 for the FTIR method. The results indicated that the GC–MS method is more selective for naphthenic acids, and that the FTIR method overestimates their concentrations.