The structures of four Ca-phosphonate phases are reported here: Ca(C6H5–PO3H)2 (1), Ca(C6H5–PO3)·2H2O (2), Ca(C4H9–PO3H)2 (3) and Ca(C4H9–PO3)·H2O (4). Structural models were obtained ab initio by using a combined synchrotron powder diffraction, solid-state nuclear magnetic resonance, and gauge including projector augmented wave (GIPAW) calculation approach. The 1H, 13C, 31P and 43Ca NMR parameters calculated from these structural models were found to be in good agreement with the experimental values, thereby indicating the high accuracy of the DFT-optimized structures. Correlations between the NMR parameters and structural features around the phosphonate were then analyzed, showing in particular the high sensitivity of the 31P asymmetry parameter ηCS and the 43Ca isotropic chemical shift to changes in local structure around the phosphonate groups and the Ca2+, respectively. Finally, the NMR data of a new mixed Na–Ca phosphonate phase, Ca1.5Na(C4H9–PO3)2, are reported.