Acidic proton modulation of a stilbene-based zwitterionic sulfonic acid in the crystalline state was studied using three amines with different pK(a) values. The three organic crystal structures prepared from the intermolecular interactions of the acid with the amines and water were solved by single-crystal X-ray crystallography. These crystals included an ammonium salt and two hydrate crystals. Furthermore, the three generated crystals could mimic three distinct biological systems: a water/proton blockade, a protonated water array, and a one-dimensional water channel.