Groundwater held within fractured rock aquifers has been shown to be obtainable from a number of vastly different geological settings, including indurated sediments, low to high-grade metamorphics, acidic and basic volcanics, and intrusive igneous rocks. This type of aquifer underlies approximately 40% of the Australian continent. Fractured rock aquifers are assuming an increasing importance for providing marginal water supplies, as the better known sedimentary aquifers become almost fully utilised. Water derived from such sources is now used for irrigation, livestock supplies, small town water supplies, and water supplies for mining and remote communities throughout Australia. Yet despite their obvious importance, very little is known about how fractured rock aquifers store and transport ground water. A lack of understanding of and predictive capability for groundwater movement within, and recharge to, fractured rock aquifers has resulted in management of such groundwater being largely problematical. The major problem is our inability to measure parameters that control the flow system (e.g. location and size of fractures). Management has often been reactionary, reliant on the results of monitoring salinity and groundwater levels to assess the health of a fractured rock system. Because of low porosity, and a large spatial and temporal variability of water levels and salinity, monitoring in fractured rock aquifers needs to occur over longer timescales than for sedimentary aquifers. By the time monitoring has detected changes in the hydraulic balance of a system, it may be politically difficult to reduce allocations to the required level. Prediction of contaminant migration is similarly difficult, but may be particularly important due to potential high transport velocities. To date, traditional methods have not been highly successful in gaining insights to the controls of movement of water and solutes in fractured rock systems. The challenge for the future is to develop new techniques which will allow improvements to our theoretical grasp on the basics of these systems. A follow-on heightened technical understanding should then underpin more successful management of these resources into the next century.