During the past decade, researchers have designed and synthesised a variety of artificial molecular pumps capable of the active transport of macrocycles (rings) from free solution into mechanically interlocked states. In their ability to drive non-equilibrium transport, these artificial molecular pumps imitate natural transmembrane transporters, which are widespread in living organisms. Despite this resemblance, ring-threading molecular pumps have not previously been operated in aqueous supramolecular assemblies in imitation of their natural counterparts. Here, we demonstrate the active transport of charged macrocycles from aqueous solution into micellar assemblies of polymer chains, which remain stable after pumping has occurred. While micelles are used routinely to encapsulate and solubilise hydrophobic small molecules in aqueous solution, this report, by contrast, shows that artificial molecular pumps can harness external energy to drive hydrophilic molecules into micelles where they are stored at concentrations far from equilibrium.