Upon burial, the organic and inorganic components of hard tissues such as bone, teeth, and tusks are subjected to various alterations as a result of interactions with the chemical milieu of soil, groundwater, and presence of microorganisms. In this study, simulation of the Ca L$_{2,3}$-edge X-ray absorption near edge structure (XANES) spectrum of hydroxyapatite, using the CTM4XAS code, reveals that the different symmetry of the two nonequivalent Ca$_{(1)}$ and Ca${(2)}$ sites in the unit cell gives rise to specific spectral features. Moreover, Ca L$_{2,3}$-edge XANES spectroscopy is applied in order to assess variations in fossil bone apatite crystallinity due to heavy bacterial alteration and catastrophic mineral dissolution, compared to well-preserved fossil apatite, fresh bone, and geologic apatite reference samples. Fossilization-induced chemical alterations are investigated by means of Ca L$_{2,3}$-edge XANES and scanning electron microscopy (SEM) and are related to histological evaluation using optical microscopy images. Finally, the variations in the bonding environment of Sr and its preference for substitution in the Ca$_{(1)}$ or Ca$_{(2)}$ sites upon increasing the Sr/Ca ratio is assessed by Sr K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy.