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.