The majority of water has vanished from modern meteorites, yet there remain signatures of water on ancient asteroids. How and when water disappeared from the asteroids is important, because the final fluid-concentrated chemical species played critical roles in the early evolution of organics and in the final minerals in meteorites. Here we show evidence of vestigial traces of water based on a nanometre-scale palaeomagnetic method, applying electron holography to the framboids in the Tagish Lake meteorite. The framboids are colloidal crystals composed of three-dimensionally ordered magnetite nanoparticles and therefore are only able to form against the repulsive force induced by the surface charge of the magnetite as a water droplet parches in microgravity. We demonstrate that the magnetites have a flux closure vortex structure, a unique magnetic configuration in nature that permits the formation of colloidal crystals just before exhaustion of water from a local system within a hydrous asteroid.