The novel concept of amphiphilic molecular motors that self-assemble into responsive supramolecular nanotubes in water is presented. The dynamic function of the molecular motor units inside the supramolecular assemblies was studied using UV-vis absorption spectroscopy and cryo-transmission electron microscopy (cryo-TEM) microscopy. Reorganization between distinct, well-defined nanotubes and vesicles can be reversibly induced by light, going through the rotation cycle of the motor, i.e. driven by alternate photochemical and thermal isomerization steps in the system. This is the first example in which a molecular rotary motor shows self-assembly in an aqueous medium with full retention of its functionality, paving the way to increasingly complex, highly dynamic artificial nanosystems in water.