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. O(o)-containing species were prevalent (>90%), O(o)S(s) were predominant (<10% relative abundance), and O(o)N(n) were least abundant in all runoff water samples. O(o)S(s) species were predominant in all the samples investigated. The heteroatomic classes present in runoff water at greater than 1% relative abundance include: O(2)N(1), O(3)N(1), O(2), O(2)S(1) O(3), O(3)S(1), O(4), O(4)S(1), O(5), O(5)S(1), O(6), O(6)S(1), O(7), O(7)S(1), O(8) and O(8)S(1). Assuming the same response factor for all O(o) species, the O(4) class, presumably dicarboxylic acids, was generally more prevalent than the O(2) class in all samples. The O(2) 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.