In order to clarify details of volatiles incorporation in arrojadites, two samples previously characterized by X-ray diffraction and electron-microprobe (EMP) and LA-ICPMS analysis were investigated by single-crystal FTIR spectroscopy. The present study confirms and makes more quantitative previous results by single-crystal structure refinement about the presence and orientation of three OH− groups (one with partial occupancy) in the arrojadite structure. The FTIR spectra showed the presence of NH4+ in arrojadite from Yukon, which was confirmed by EMP analysis (ca. 700 ppm N). Micro FTIR imaging was used to check the homogeneity of OH and NH4+ across the examined samples, as a prerequisite for the single-crystal polarized study. Based on the hydrogen bonding environment determined by structure refinement, the bands observed in the 3600–3500 cm−1 region can be assigned to the OH1 (at lower frequency) and OH2 (at higher frequency) dipoles. In the spectrum of arrojadite from Yukon several hyperfine components are resolved; these can be assigned to local Mg/ Fe2+ octahedral configurations at the OH-coordinated octahedra. Both spectra show a very broad absorption extending from ~ 3500 to 2500 cm−1 which is assigned to the OH3 hydroxyl group. The orientation of the O-H dipoles calculated from the FTIR absorbance data are in excellent agreement with those calculated from the refined atomic coordinates, confirming the validity of the latter method also in the case of low-Z elements. Assuming the water content derived from EMP analysis, an integrated molar coefficient (polarized data) ɛI = 63937 l/(mol·cm2) is calculated for the spectroscopic quantification of H2O in arrojadite. For N, based on the EMP analysis, we obtain (for unpolarized data in the N-O bending region) ɛi = 11000 ± 2000 l/(mol·cm2) and ɛI = 300 ± 60 l/(mol·cm2) from integrated and linear intensity data, respectively.