Molecular dynamics (MD) simulations at several different temperatures were run to investigate the transport, adsorption, and stability of carbon dioxide (CO2) and water phases in contact with a calcite surface. All simulated systems showed evidence of CO2 transport and interface stability heavily affected by the presence of calcite and the simulation temperature. The number of CO2 molecules that successfully traversed the water layer and adsorbed on the calcite surface increased with temperature, while the adsorption stability (indicated by the adsorption energy) decreased. It was found that the short-range potential has a significant impact on the preferred CO2 orientation and adsorption selectivity. Carbon dioxide tended to fill partial hydrate cavities at the water–hydrate interface, potentially promoting the formation of new hydrate. These findings indicate the need to consider the implications that CO2 injection will have for reservoirs with pre-existing clathrate hydrates.