There is interest in using mature fine tailings (MFT) in reclamation strategies of oil sands mining operations. However, simulated runoff from different dried MFT treatments is known to have elevated levels of salts, toxic ions, and naphthenic acids, and alkaline pH and it is phytotoxic to the emergent macrophyte, common reed (Phragmites australis). Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) of the acidic species in the runoff confirmed that the distribution of oil sands naphthenic acids and associated oil sand acids was dependent on the MFT treatment. Furthermore, FT-ICR MS studies of the acidic species in hydroponic systems revealed that there was no plant-mediated change in the electrospray ionization mass spectra of the runoff. Oo-containing species were prevalent (>90%), OoSs were predominant (<10% relative abundance), and OoNn were least abundant in all runoff water samples. OoSs species were predominant in all the samples investigated. The heteroatomic classes present in runoff water at greater than 1% relative abundance include: O2N1, O3N1, O2, O2S1 O3, O3S1, O4, O4S1, O5, O5S1, O6, O6S1, O7, O7S1, O8 and O8S1. Assuming the same response factor for all Oo species, the O4 class, presumably dicarboxylic acids, was generally more prevalent than the O2 class in all samples. The O2 class is indicative of classical naphthenic acids. However, dicarboxylic acids will form negative ions more readily than the monocarboxylic acids as there are two acidic hydrogens available for formation of these species. Copyright © 2010 John Wiley & Sons, Ltd.