The structure and spectroscopic properties of selected models of B-type carbonate defects in apatite locally compensated by fluoride or hydroxyl ions are investigated using first-principles quantum mechanical calculations. Theoretical infrared absorption spectra and 13C, and 19F nuclear magnetic resonance chemical shifts are determined. Among the investigated models, only the clumped (CO3 2−, F−) defect, with the carbonate group close to the sloping face of the tetrahedral site and the F− ion at the remaining apex, corresponds to previous experimental observations performed on carbonate-fluorapatite samples. Although the substitution of hydroxyl by fluoride ions is commonly observed in minerals, the clumped (CO3 2−, OH−) defects are unlikely to occur in apatite, considering both their theoretical spectroscopic properties and relative stability. Anionic F− for OH− exchange between channel and B sites displays a preference of ~20 kJ/mol for the local charge compensation by fluoride ions at the B-site, pointing to a significantly different behavior of F− and OH− ions in the charge compensation mechanism. This difference is ascribed to the poor H-bond acceptor character of available oxygen atoms surrounding the apex of the tetrahedral site. The explicit calculation of the infrared absorption spectra of the defect models is also used to interpret the significant difference observed in the linewidth of the ν2 and ν3 CO3 infrared powder absorption bands of carbonated apatite samples. It is shown that for a concentration of 4.4 wt% of CO2, long-range electrostatic effects already significantly contribute to the broadening of the ν3 CO3 bands in apatite