The structure relaxation mechanism of the fluorapatite (100) surface under completely hydrated ambient conditions has been investigated with the grazing incidence X-ray diffraction (GIXRD) technique. Detailed information on lateral as well as perpendicular ordering corresponding to the water molecules and atomic relaxations of the (100) surface of fluorapatite (FAp) crystal was obtained from the experimental analysis of the CTR intensities. Two laterally ordered water layers are present at the water/mineral interface. The first layer consists of four water molecules located at 1.6(1) A above the relaxed fluorapatite (100) surface while the second shows the presence of only two water molecules at a distance of 3.18(10) A from the mineral surface. Thus, the first layer water molecules complete the truncated coordination sites of the topmost surface Ca atoms, while the second water layer molecules remain bonded by means of H-bonding to the first layer molecules and the surface phosphate groups. Molecular mechanics simulations using force field techniques are in good agreement with this general structural behavior determined from the experiment.