Abstract The Eastern Cape Karoo region is water stressed and will become increasingly so with further climate change. Effective and reliable groundwater management is crucial for a development such as the proposed hydraulic fracturing for shale gas. This is especially critical across this region of agriculture and protected ecosystem services. The research, as part of baseline data gathering, aims to characterize the hydrochemistry for both the shallow groundwater (<500 m) and saline groundwater closer to the c. 2–5 km deep shale gas. The classification will be used to determine possible vertical hydraulic connectivity between the shallow and deep aquifers, prior to anticipated hydraulic fracturing. This paper reports on the baseline framework that includes the sampling design and a hydrocensus with field-recorded parameters shown as interpolated maps. This includes electrical conductivity, groundwater level and borehole yield. Together with completed sampling results, these data provide a record against which the environmental impact of hydraulic fracturing and the reinjection of production water can be determined. The research is a critical first step towards the successful governance of groundwater in light of proposed shale gas development in the Karoo. In its absence, effective regulation of the sector will not be effective.