The incorporation of foreign ions, such as Mg2+, exhibiting a biological activity for bone regeneration is presently considered as a promising route for increasing the bioactivity of bone-engineering scaffolds. In this work, the morphology, structure, and surface hydration of biomimetic nanocrystalline apatites were investigated before and after surface exchange with such Mg2+ ions, by combining chemical alterations (ion exchange, H2O-D2O exchanges) and physical examinations (Fourier transform infrared spectroscopy (FTIR) and high-resolution transmission electron microscopy (HRTEM)). HRTEM data suggested that the Mg2+/Ca2+ exchange process did not affect the morphology and surface topology of the apatite nanocrystals significantly, while a new phase, likely a hydrated calcium and/or magnesium phosphate, was formed in small amount for high Mg concentrations. Near-infrared (NIR) and medium-infrared (MIR) spectroscopies indicated that the samples enriched with Mg2+ were found to retain more water at their surface than the Mg-free sample, both at the level of H2O coordinated to cations and adsorbed in the form of multilayers. Additionally, the H-bonding network in defective subsurface layers was also noticeably modified, indicating that the Mg2+/Ca2+ exchange involved was not limited to the surface. This work is intended to widen the present knowledge on Mg-enriched calcium phosphate-based bioactive materials intended for bone repair applications.