The water produced during the extraction of bitumen from oil sands is toxic to aquatic organisms due largely to a group of naturally occurring organic acids, naphthenic acids (NAs), that are solubilized from the bitumen during processing. NAs are a complex mixture of alkyl-substituted acyclic and cycloaliphatic carboxylic acids, with the general chemical formula CnH(2n + Z)O2, where n is the carbon number and Z specifies a homologous family. Gas chromatography-electron impact mass spectrometry was used to characterize NAs in nine water samples derived from oil sands extraction processes. For each sample, the analysis provided the relative abundances for up to 156 base peaks, with each representing at least one NA structure. Plotting the relative abundances of NAs as three-dimensional bar graphs showed differences among samples. The relative abundance of NAs with carbon numbers < or = 21 to those in the "C22 + cluster" (sum of all NAs with carbon numbers > or = 22 in Z families 0 to -12) proved useful for comparing the water samples that had a range of toxicities. A decrease in toxicity of process-affected waters accompanied an increase in the proportion of NAs in the "C22 + cluster", likely caused by biodegradation of NAs with carbon numbers of < or = 21. In addition, an increase in the proportion of NAs in the "C22 + cluster" accompanied a decrease in the total NAs in the process-affected waters, again suggesting the selective removal of NAs with carbon numbers of < or = 21. This is the first investigation in which changes in the fingerprint of the NA fraction of process-affected waters from the oil sands operations has corresponded with measured toxicity in these waters.