Abstract The dissolution of hydroxyapatite (HAP) and fluorapatite (FAP) has been studied (25 °C, 0.1 M NaCl medium) within the pH ranges 2–11 (FAP) and 4–10 (HAP). A range of techniques has been utilized to achieve understanding in how these two abundant minerals may interact with their natural surroundings (e.g., body fluids and soil environments). Synthetic crystalline HAP and FAP were prepared, and both minerals were found to undergo a phase transformation generated during a dialysis step of the synthetic routes. Surface-deficient layers with the nonstoichiometric compositions Ca8.4(HPO4)1.6(PO4)4.4(OH)0.4 and Ca9(HPO4)2(PO4)4F2 were identified. The equilibrium analysis of experimental solubility data of the two apatite systems was based upon potentiometric titration data, batch experiments, and zeta-potential measurements in combination with information provided by X-ray photoelectron spectroscopy (XPS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. The analysis required, besides the two solubility equilibria, the formation of surface protonation/deprotonation reactions, re-adsorption processes involving phosphate and fluoride ions as well as an ion exchange reaction (≡F + H2O ⇋ ≡OH + H+ + F–) to fully describe the dissolution characteristics of the two apatite systems. The resulting model also agrees with observations from XPS and solubility data, claiming the formation of CaF2(s) in the most acidic pH range of the FAP system. In addition, calculated isoelectric points (pHiep) are in agreement with values from surface charge measurements showing pHiep (HAP) = 8.1 and pHiep (FAP) = 5.7.