Magnesium ion channels and transporters regulate the cellular concentrations of Mg2+, which must be tightly controlled as imbalances have been associated with diseases such as osteoporosis, diabetes, and high blood pressure in humans. The channels and transporters allow the "native" Mg2+ to be transported against a high background concentration of its major competitor, Ca. Their selectivity filters (the narrowest part of the open pore) control metal ion selectivity. As the structures of Mg2+ channels in an open conformation with bound Mg have not yet been solved, the key determinants of Mg2+/Ca2+ selectivity in Mg2+ ion channels remain elusive. Here, using density functional theory combined with continuum dielectric methods, we evaluated how the competition between Mg2+ and Ca2+ in model selectivity filters depends on the degree of metal hydration, which correlates with the pore size/rigidity as well as the composition and solvent accessibility of the selectivity filter. The key determinant of the selectivity for Mg2+ over Ca2+ in the Mg' channel selectivity filter is a pore that is sufficiently large to accommodate hexahydrated Mg ions. In such wide pores, the hexahydrated metal ions interact indirectly with the protein ligands, hence metal desolvation and ligand ligand steric repulsion become less important than Mg' water protein interactions. These wide pores are Mg2+-selective because compared to Ca2+ or Na+ and K+ monocations, Mg2+ better polarizes the bound water molecules resulting in stronger Mg' water protein interactions. Although both tetrameric and pentameric filters with pores that can accommodate hexahydrated metal ions could select Mg2+ over Ca', a bilayered pentameric filter lined with a ring of amides and a ring of carboxylates seems to best discriminate the "native" Mg2+ from its key rival, Ca2+. Our results are consistent with available experimental data and help to elucidate the selectivity filters in the Mg2+-selective TRPM6 and CorA channels.