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In the Beer Sheva region of the Negev desert, the only significant fresh groundwater is contained within the Judea Group carbonate aquifer. It is found that this aquifer holds two distinctly different old water bodies. One such groundwater body has evolved in equilibrium with the carbonate aquifer rocks after being recharged during the Holocene in the Hebron Mountains north of the study area. At present, modern recharge, as denoted by the tritium and radiocarbon contents, is very minor. A subtle ’piston effect’ generated by contemporary replenishment is discussed in representative hydrographs in Beer Sheva wells. Another groundwater body identified in the Judea Group aquifer derives from the underlying Kurnub Group aquifer. The regional artesian Kurnub Group aquifer (Nubian Sandstone) contains an older and brackish groundwater body which has been recharged in Sinai during Pleistocene pluvials. Faulting in the Beer Sheva region facilitated hydrologic contact between the two aquifers. Exploitation of the Judea Group has released confining pressures and resulted in the intrusion of Kurnub Group water into the overlying Judea Group carbonate aquifer. This process is most significant in those wells drilled close to major faults where salinity increases with pumping. The intruding water originating from the Kurnub Group sandstone aquifer has not yet equilibrated chemically with the carbonate host. The low pH and high temperatures that have been encountered indicate continuing and very recent intrusion. In the Beer Sheva area, in the absence of direct significant modern recharge (as determined from tritium and C-14 values), all waters should be considered as paleowaters that are being mined. A complete revision of the hydrologic concept by which the multiple aquifer system can be exploited is required, to take into account the fact that the fresh Judea Group groundwater is actually an old (Holocene) water body intruded by brackish and older (Pleistocene) water along fault zones.