For managed aquifer recharge (MAR) to succeed, an aquifer is needed which allows easy access to a relatively high storage capacity. Whereas the country rock hosting theWindhoek Aquifer, consisting largely of quartzite, has no primary porosity, secondary porosity developed for several reasons. The brittle nature of the quartzite led to better secondary porosity development than in the adjacent schistose terrain. The degree and intensity of fracturing decreases as the mica content of the quartzite increases. Therefore, a larger storage capacity is found per unit volume of the fractured quartzite compared to an equal volume of fractured schist. Equally, the success of MAR depends on a thorough understanding of the ambient water quality in the various parts of the aquifer together with potential water-rock interactions. This study was aimed at developing water quality guidelines with specific management options for ensuring sustainable artificial recharge of the aquifer. Ample groundwater quality data are available for the saturated zone but a major aspect that can only be assessed to a limited extent is the water-rock interactions that will take place when the unsaturated zone becomes saturated during injection. To some extent unsaturated water-rock interaction can be inferred from the hydrochemistry of the saturated zone and its evolution in the aquifer. Water quality criteria for the recharge water are included. Keywords: artificial recharge, hydrochemistry, Namibia, quartzite, Windhoek.