Jointed quartzites of the NW-dipping Auas and Kleine Kuppe formations together with cross-cutting faults form an interconnected, fractured aquifer network that is in part compartmentalised. The faults have a significantly higher permeability than the quartzites and large-fragment fault breccias are often highly permeably in depth. The 2016/2017 drilling programme was aimed at tapping the faults down to the depth of 400 m in localities close to existing infrastructure. Resistivity and magneto-telluric surveys perpendicular to faults were followed by the drilling of inclined, reverse-circulation probe boreholes to determine accurately the dip of faults. All boreholes deviated from their initial start orientations. Production holes were sited according to fault dip and to expected borehole deviation. Hydrothermal alteration of country rocks adjacent to the faults and mineral precipitation are ascribed to the thermal effects of the 52-Ma Aris Suite trachytes. Boreholes were sampled every metre and comprehensive records were taken. The Windhoek Aquifer is a closed system that cannot lose much water in any direction underground. It is an outstanding water reserve in times of need. However, it has been exploited at a rate far greater than the rate of natural recharge and artificial recharge is essential to replenish it and to ensure the availability of emergency water supplies during future droughts. The drilled production boreholes form part of the implementation of the Windhoek Managed Aquifer Recharge Scheme (WMARS) which is based on the premise of over-abstracting water from the Windhoek Aquifer during periods of extended drought and recharging the aquifer with water supplied from the three-dam system blended with potable reclaimed water. Keywords: Windhoek aquifer, Groundwater, Faulting, Drilling, Water management, Auas Formation, Kleine Kuppe Formation.