Amphiphilic small molecules and polymers produce diverse nanostructures in an aqueous medium. Emerging reports suggest that there is a great opportunity to enrich the structure and function of amphiphilic aggregates by suitable molecular engineering in the building block to enable directional non-covalent interaction based on specific molecular recognition to circumvent the immiscibility driven aggregation governed by the critical packing parameter. This review discusses representative recent examples on self-assembly of small molecule and polymeric amphiphiles by H-bonding interaction in an aqueous medium. The specific impact of H-bonding on regulating morphology, stability, dynamics, thermodynamics, surface functional group display, stimuli-responsiveness and precision of amphiphilic nanostructures has been highlighted and correlated with their potential application as supramolecular biomaterials.