The potential for sorption and possible degradation of components in oil sands processed water (OSPW) by the use of synthetically engineered co-polymers is receiving growing attention. Recent research has highlighted the sorption of total oil sands naphthenic acid fraction components (NAFCs) by β-cyclodextrin (β-CD) co-polymers. The incorporation of β-CD within co-polymer frameworks represents a novel modular approach with significant potential for controlled tuning of the textural mesoporosity of the sorbents. Herein, we report the Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) characterization of aqueous samples containing oil sands NAFCs following sorption with a range of cyclodextrin-based co-polymers. The materials investigated were β-CD cross-linked with three different types of diisocyanates, namely, (i) 4,4′-dicyclohexylmethane diisocyanate, (ii) 4,4′-diphenylmethane diisocyanate, and (iii) 1,4-phenylene diisocyanate. Variable sorption of NAFCs was observed according to the cross-linking density of the co-polymer framework and the nature of the cross-linker unit. Furthermore, the sorption of the NAFCs by the co-polymers was not affected by other parameters, such as metal ions, salinity, and non-oil sands acid fractions present in OSPW. The observation of molecular selective sorption in co-polymer materials containing β-CD represents an important contribution toward the development of sorbent materials for the controlled removal of oil sands acids in aquatic environments. The FT-ICR MS measurements also contribute further to the understanding of the thermodynamic sorption mechanism of such materials.