Supramolecular architectures with the synchronized combination of various directional noncovalent forces arc ubiquitous in biological systems. However, reports of such abiotic synthetic systems involving H-bonding in aqueous medium are rare due to the challenge faced in the formation of such structures by overcoming the competition from the water molecules. In this paper we have studied self-assembly of two structurally related naphthalene-diimide (NDI) conjugated bola-amphiphiles (NDI-1 and NDI-2) in water with an aim to realize the specific role of H-bonding among the hydrazide units present in one of the two building blocks (NDI-2) on the self-assembly. Both chromophores showed vesicular assembly in aqueous solution driven primarily by pi-stacking among the NDI chromophores, which could be probed by UV-vis absorption spectra. Contrary to common belief, the lack of an H-bonding group in NDI-1 was found to be a boon in disguise in terms of the stability of the aggregates. Whereas NDI-2 aggregates showed LCST around 65-70 degrees C owing to the breaking of the H-bonds with increased temperature, the NDI-1 aggregates were found to be structurally intact until 90 C, which may be attributed to the increased hydrophobicity introduced by the absence of the polar hydrazide group. Further concentration- and solvent-dependent UV-vis studies showed that NDI-1 formed assembled structure at greatly dilute solution and also in a solvent such as THF, confirming greater propensity for its self-assembly. As both bola-amphiphiles contain an electron-deficient NDI chromophore, interaction of their vesicles was studied with an externally added electron-rich pyrene derivative. Surprisingly, NDI-1 did not show any charge-transfer interaction with the donor, whereas NDI-2 could effectively intercalate, leading to a functional membrane with tunable surface functionalities. This was attributed to the additional stability of the intercalated state by H-bonding among the hydrazide units.