The intercalation of non-aqueous fluids in the nanopores of organic and inorganic materials is of significant interest, particularly in the energy science community. Recently, XRD and computational modeling results have shown that structural Ffor OHsubstitution in layered silicates makes them more hydrophobic. Here, we use Grand Canonical Molecular Dynamics (GCMD) calculations to investigate how increasing the F-/(F-+OH-) ratio of a prototypical layered silicate (the smectite Na-hectorite) impacts the intercalation behavior of CO2 and H2O at elevated temperature and pressure. At the conditions of this study (T = 323 K, P = 90 bar, water-saturated CO2), increasing Ffor OHsubstitution causes decreasing total CO2+H2O intercalation, increasing CO2/(CO2+H2O) ratios in the interlayer galleries, and an increasing energy barrier to CO2 and H2O intercalation. CO2 intercalation is greatest at monolayer basal spacings, and the results support the idea that with Na + as the exchangeable cation the interlayers must be propped open by some H2O molecules to allow CO2 to enter the interlayer galleries. The computed immersion energies suggest that the bilayer or a more expanded structure is the stable state under these conditions, in agreement with experimental results, and that the basal spacings of the minimum energy 2L structures increase with increasing Ffor OHsubstitution. These results are consistent with a wide range of experimental data for smectites at ambient conditions and elevated pressures and temperatures and suggest that Ffor OHsubstitution in conjunction with reduced structural charge and exchange with large, low charge cations may increase the ability of smectite minerals to incorporate hydrophobic species such as CH4, CO2, H2, and other organic compounds.