The standard model of enhanced ionic conductivities in solid electrolyte heterostructures follows from a continuum mean-field description of defect distributions that makes no reference to crystalline structure. To examine ionic transport and defect distributions while explicitly accounting for ion—ion correlations and lattice effects, we have performed molecular dynamics simulations of a model coherent fluorite heterostructure without any extrinsic defects, with a difference in standard chemical potentials of mobile fluoride ions between phases induced by an external potential. Increasing the offset in fluoride ion standard chemical potentials across the internal interfaces decreases the activation energies for ionic conductivity and diffusion and strongly enhances fluoride ion mobilities and defect concentrations near the heterostructure interfaces. Non-charge-neutral “space-charge” regions, however, extend only a few atomic spacings from the interface, suggesting a continuum model may be inappropriate. Defect distributions are qualitatively inconsistent with the predictions of the continuum mean-field model, and indicate strong lattice-mediated defect–defect interactions. We identify an atomic-scale “Frenkel polarisation” mechanism for the interfacial enhancement in ionic mobility, where preferentially oriented associated Frenkel pairs form at the interface and promote local ion mobility via concerted diffusion processes.