Nuclear energy currently contributes about 10% of the world’s electricity supply but, at present, there are only interim storage facilities for the accumulated 2.6 x 108 kg of spent nuclear fuel. Geological storage is the universally favoured option for permanent removal of this highly radioactive waste from the biosphere with the first purpose-designed and constructed permanent disposal site, the Onkalo facility in Finland, expected to become operational in the next few years. Envisioned and planned geological disposal facilities for high-level radioactive waste will commonly include a bentonite clay buffer called the Engineered Barrier System (EBS); this flow barrier both surrounds the waste cannisters and backfills the disposal galleries. However, questions are being raised about the long-term performance of bentonite for waste containment due to specific issues associated with inhomogeneous fluid-rock interaction occurring within the material. We apply a novel combination of μ-MRI methods and 2H labels to monitor flow in barrier materials in unprecedented detail and resolution to reveal micro-scale fluid-flow variations caused by nano- and microheterogeneities not possible via other techniques. We demonstrate the fluid penetration front becomes fragmented, and that fragmentation is governed by heterogeneities in the clay’s pore structure; both must be considered in host rock characterisation and long-term EBS design, manufacture, and performance.