This work concerns the analysis of model naphthenic acids and authentic naphthenic acids from the tailings ponds of the Athabasca tar sands. A first objective was to compare atmospheric pressure chemical ionization mass spectrometry (APCI-MS) with the previously studied electrospray mass spectrometry (ESI-MS) in this analysis. APCI-MS had a wider range of quantitation than ESI-MS, but its detection limit was poorer and model compounds showed greater variation in calibration sensitivity. A second objective was fractionation of naphthenic acids from tailings pond water and analysis by the Microtox toxicity assay. Fractionation on the basis of solubility gave fractions that did not differ significantly either in their congener distribution by ESI-MS or in their response to the Microtox assay. When partial separation was achieved by anion exchange chromatography, fractions with a higher proportion of multi-ring structures exhibited lower toxic potency. This finding is consistent with field observations that indicate that the toxic potency of tailings ponds water declines as the samples age-multi-ring structures are more highly branched and therefore more resistant to microbial degradation.