At most contaminated sites in fractured rock, the off-site migration of aqueous-phase contaminants are governed by the distribution of hydraulic head and the arrangement of discrete fracture pathways. The cost of characterizing the groundwater flow system in such environments is often much higher than for equivalently-scaled porous media. Thus, inexpensive borehole geophysical techniques are often utilized as an efficient means by which to obtain information on the flow pathways. In many cases, borehole geophysics is the only hydrogeological information obtained from the boreholes. Thus, some uncertainty in the interpretation of the groundwater flow system will accrue. To explore this, several standard (electric and gamma) and fracture-specific (caliper, conductivity, temperature, differential temperature, and video) logs were collected from boreholes in which detailed hydraulic characterization had also been conducted. The hydraulic characterization included hydraulic testing conducted using a 0.5 m packer spacing, the measurement of groundwater velocity using point dilution, and time-series measurement of hydraulic head obtained from multilevel borehole completions. The study was conducted in a flat-lying dolostone of Silurian age and relatively uniform composition, where 5-8 major horizontal fracture features govern the predominantly horizontal flow system. The results show that the caliper log, which is often used to identify open fracture features was found to identify some open fractures where weak rock had resulted in spalling of the borehole wall, but missed many of the major open fractures that dominate the flow system. Similarly, interpretation of hydraulically active fractures from differential temperature and conductivity measurements was found to be poorly correlated to zones of high transmissivity. Many large-aperture fractures having low groundwater velocities were found to have un-interpretable caliper, temperature and conductivity signatures.