Abstract Ashalim maze cave, and neighbouring caves in the NW Negev Desert, Israel demonstrate hypogene karst features. These features are shown to have developed as a result of the mixing of two types of groundwater flowing in opposite directions within two tiers of Cretaceous rock aquifers. The stable isotope composition indicates that the lower Kurnub sandstone aquifer was recharged over far-field Nubian Sandstone outcrops in the vicinity of the Precambrian basement outcrops of the Sinai Desert, which belongs to the Afro-Arabian dome. The water flows northward and rises into the Judea carbonate aquifer through deep faults. A similar hydrogeological system is inferred for the speleogenetic period of Ashalim Cave. Dewatering of the cave occurred in the Pliocene due to regional uplift. This is indicated by the first vadose speleothems, dated to the late Pliocene (3.1 Ma). This was followed by surface denudation, which breached the cave and formed the present entrance.