Four types of thermal groundwater in Jordan were distinguished by Y and rare earth elements (REY) distribution patterns. Complementary to the stratigraphic origin of water in springs or of wells, REY patterns identify either recharge areas covered by basalt, limestones or sandstone, or interaction with basalt-limestone contact zones. This hydrochemical grouping does not always correspond with “common geological knowledge” of the aquifer lithology of the thermal water. Therefore, comparison of the hydrochemical signatures of REY patterns and the lithological source of water yield insight into transaquifer flow. Out of 44 analysed groundwater, 18 indicated down- and 3 upflow of water the latter due to step faults near the Rift system. During transaquifer flow REY patterns of groundwater from basalts and gypsum beds or gypsum-cemented sandstones are not changed by subsequent interaction with limestones, whereas in groundwater originating from dissolution of chalk and limestones REY patterns are adjusted to those typical for gypsum-bearing sediments. Cross plots of δ¹⁸O vs. δ²H reveal essentially two trends. The main trend of water from limestone aquifers define a mixing line of past to recent meteoric water with negligible contributions of Pleistocene water. Some water from Eocene aquifers plot on the local Mediterranean meteoric water line, others plot together with water from sandstone aquifers at enhanced δ¹⁸O values due to hydrothermal overprinting.