Generic approaches for determining the spatial and temporal variability of a fault's hydrogeological properties are being developed by studying the reversed Tsukiyoshi Fault at Tono, central Japan. This fault is associated with zones of deformation/damage that are sometimes wider than the fault's displacement. The hydraulic characteristics probably vary laterally over metres to tens of metres and the hanging wall and foot wall have different hydraulic properties. It is also possible that some of these properties may have changed over time, due to physical processes and/or to water/rock interactions, even at relatively low-temperatures and pressures (to a few tens of degrees centigrade and hundreds of bars). It is suggested that mineralogical and structural data can be used to estimate the most transmissive conditions within a fault in the past. These estimates can then be used to select conservative (‘worst-case’) fault parameters for assessing the future safety of underground waste repositories. Such information can also be used to design a repository to avoid faults with permeable crush zones. The study demonstrates the value of integrating detailed mineralogical and petrological studies into a borehole drilling programme for characterizing the hydraulic properties of faults.