The diverse assembly of encapsulated water molecules in hybrid bisamide hosts has been investigated. Hybrid bisamides containing aromatic terminal groups and flexible aliphatic spacers restrict the intermolecular amide–amide hydrogen bonding and π-stacking interactions. However, the addition of water promotes the self-assembly processes by bridging between the bisamide molecules and the stabilized helical or zigzag one dimensional water chains. The bisamide 1 containing ethylenediamine adopted an extended shape and stabilized one-dimensional hydrogen bonded helical water chain inside the supramolecular frameworks. In contrast, bisamide 2 containing trimethylenediamine adopted a U-shape structure and entrapped an isolated water molecule. X-ray crystallography reveals that the bisamide 4 containing cadaverine adopted an extended structure and a stabilized one-dimensional hydrogen bonded zigzag water chain in a higher order packing. Moreover, by U-tube experiments using the pH gradient as the driving force across a liquid chloroform phase, bisamide 4 was found to be considerably active proton transporter than bisamide 1.