We analyzed maze caves and the associated hydrogeology in the northern Negev–Judean Desert in Israel to provide insight on fluid migration and porosity development, with relevance to groundwater and petroleum reservoirs on the Arabian Platform flanks. The caves occur specifically in the arid region of the southern Levant, with no equivalent in the moister climate areas further to the north. The karstified bedrock consists of Upper Cretaceous epicontinental carbonates. Caves were formed mainly above deep faults associated with the Syrian arc fold system. Hypogenic flow is shown to have formed the maze caves particularly under the confinement of thick chalk and marl cap rock. Speleogenesis occurred during the Oligocene–early Miocene when the Afro-Arabian dome was rising and became erosionally truncated. Calcite deposits depleted in 18O point to a connection between the caves and recharge over far-field Nubian Sandstone outcrops, north of the Precambrian basement outcrops on the eastern side of the Red Sea. During the early–middle Miocene, the Dead Sea rift began dissecting the region, forming a deep endorheic depression at the eastern margin of the study area and disconnecting the far-field groundwater flow. This was followed by subsiding groundwater levels and associated dewatering of the caves. Fault escarpments and canyon downcutting then dissected the caves, forming the present entrances. The caves are currently mostly dry, with scarce speleothem occurrences. Gypsum crusts with δ34SSO4 values lower than other sulfate deposits point to bacterial sulfur reduction, hydrogen sulfide, and sulfuric acid being involved in the speleogenesis.