Self-assembly by means of coordinative bond formation has opened up opportunities for the high-yield synthesis of molecules with complex topologies. However, the preparation of purely covalent molecular architectures in aqueous media has remained a challenging task. Here, we present the preparation of a three-dimensional catenane through a self-assembly process that relies on the formation of dynamic hydrazone linkages in an acidic aqueous medium. The quantitative synthesis process and the mechanically interlocked structure of the resulting catenane were established by NMR spectroscopy, mass spectrometry, X-ray crystallography and HPLC studies. In addition, the labile hydrazone linkages of the individual [2]catenane components may be 'locked' by increasing the pH of the solution, yielding a relatively kinetically stable molecule. The present study thus details a simple approach to the creation and control of complex molecular architectures under reaction conditions that mimic biological milieux.