Grand Canonical Molecular Dynamics (GCMD) simulations were performed to investigate the intercalation of CO2 and H2O molecules in the interlayers of the smectite clay, Na-hectorite, at temperatures and pressures relevant to petroleum reservoir and geological carbon sequestration conditions and in equilibrium with H2O-saturated CO2. The computed adsorption isotherms indicate that CO2 molecules enter the interlayer space of Na-hectorite only when it is hydrated with approximately three H2O molecules per unit cell. The computed immersion energies show that the bilayer hydrate structure (2WL) contains less CO2 than the monolayer structure (1WL) but that the 2WL hydrate is the most thermodynamically stable state, consistent with experimental results for a similar Na-montmorillonite smectite. Under all T and P conditions examined (323–368 K and 90–150 bar), the CO2 molecules are adsorbed at the midplane of clay interlayers for the 1WL structure and closer to one of the basal surfaces for the 2WL structure. Interlayer CO2 molecules are dynamically less restricted in the 2WL structures. The CO2 molecules are preferentially located near basal surface oxygen atoms and H2O molecules rather than in coordination with Na+ ions. Accounting for the orientation and flexibility of the structural −OH groups of the clay layer has a significant effect on the details of the computed structure and dynamics of H2O and CO2 molecules but does not affect the overall trends with changing basal spacing or the principal structural and dynamical conclusions. Temperature and pressure in the ranges examined have little effect on the principal structural and energetic conclusions, but the rates of dynamical processes increase with increasing temperature, as expected.