The syntheses and structures of ammonium salts of the active pharmaceutical agent (4-aminium-1-hydroxybutylidine)-1,1-bisphosphonic acid (alendronic acid, LH5) have been examined. Three deprotonation states of the parent acid were achieved i. e. LH4−, LH32− and LH23−, and crystallisation gave a total of six different structural phases including [NH4][LH4] ⋅ 2(H2O) as two polymorphs 1 a and 1 b, two hydrates of [NH4]2[LH3] ⋅ x(H2O), x=3 (2), x=6 (3), [NH4]5[LH3][LH2] ⋅ 8(H2O) (4) and [NH4]3[LH2] ⋅ 3(H2O) (5). The crystal structures obtained, along with that of the parent acid, enable a direct comparison of competing supramolecular synthons, involving phosphonate-phosphonate O−H⋅⋅⋅O and ammonium-phosphonate N−H⋅⋅⋅O hydrogen bonds, in a series displaying progressively decreasing P-OH with concomitantly increasing RNH3+ moieties. Indeed, the structures show some consistent connectivity patterns of the alendronate units, which thus assemble into substructures such as 2-D sheets (LH5 ⋅ H2O, 1 a), zig-zag chains (2, 5) or ladder-like arrays (3, 4). The occurrence of these motifs appears to correlate with the ionisation level of the parent acid.