We report the results of a molecular dynamics simulation study aiming to understand the interfacial structure in ceria/zirconia superlattices and the impact of the interfaces on the energies of oxygen vacancy formation and Gd ion substitution in ceria and zirconia layers of the superlattice structure. It is found that the semi-coherent interface is characterized by misfit dislocations, paired at approximately 3-4 nm, with stacking-fault-like region in between, which agrees with the TEM observations. It is also found that the vacancy formation energy and the Gd substitution energy vary as a function of distance from the interface in the individual layers, and that these energies depend on the layer thickness. In addition, the simulations showed that the defect energy variations across the thickness of the ceria and zirconia layers are consistent with the XPS data for composition profile in the superlattice structure. Finally, in the semi-coherent superlattice structure, the formation energy of oxygen vacancies and the Gd substitution energy are found to depend on the position of these defects relative to the interfacial dislocation core. In particular, the oxygen vacancy formation energy is found to be negative close to the dislocation core, indicating that vacancy concentration will increase in such regions allowing for high conduction parallel to the interface.