Suitable subsurface repositories for spent nuclear fuel are presently under investigation at several national underground research laboratories that have been excavated for this purpose. However, since spent fuel storage canisters can be expected to break down after a period of time, engineered barriers have been proposed to prevent radionuclides, leached from the canisters by groundwater, from escaping into the environment. Serious investigation of the effect of microbial activity on these barriers and the surrounding geosphere has only been undertaken fairly recently. This research has now provided evidence that most subsurface groundwater environments are reducing, due to the presence of indigenous microbial ecosystems. If such a reducing environment can be maintained during excavation, emplacement and storage of the waste canisters it could ensure that most of the radionuclides are in the reduced state, in which case, as the majority are only slightly soluble, they are unlikely to be very mobile in the groundwater system. Geological analogues at Cigar Lake, Canada, and Oklo, Gabon demonstrate that uranium ore and its fission products can be retained in situ for more than a billion years. Furthermore excavation of the laboratory at Äspö in Sweden has shown that, although the subsurface environment was disturbed during excavation, the indigenous microbial community was able to maintain the environment in a reduced state. Thus it appears to be important to characterize the natural ecosystem as well as the hydrological regime present in the subsurface sites that are being considered for storage. Natural rock barriers, which contain the indigenous groundwater and microorganisms, may provide a more resilient protection to the movement of radionuclides than that of the proposed engineered barriers.