Abstract Managing transboundary groundwater resources requires accurate and detailed knowledge of aquifers and groundwater bodies. The Pannonian Basin is the largest intracontinental basin in Europe with a continuous succession of more than 7km of Miocene to Quaternary sediments and with an average geothermal gradient of about 5°C/100m. Geographically the Pannonian basin overlaps eight countries (Hungary, Romania, Serbia, Croatia, Slovenia, Austria, Slovakia and Ukraine), so the issue of transboundary cold and thermal water resources is regionally very important. The T-JAM bilateral Hungarian–Slovenian (HU–SLO) project is the first to apply modern isotopic and chemical analyses in the characterization and correlation of a number of shared groundwater resources in the Mura-Zala Sub-basin of the Pannonian. The aims of this work were the identification of groundwater flow paths, the delineation of transboundary aquifers based on thermal and cold groundwater geochemical and isotope properties in the Mura-Zala Basin, and providing input to calibrate a hydraulic numerical model. Following a common groundwater sampling campaign, 24 cold and thermal groundwater samples from seven aquifers were collected for chemical, isotope, gas and noble gas analyses. Chemical analyses, and D, O and C isotopes were used to correlate cross border aquifers. A regional groundwater flow is hydrogeologically possible in some aquifers in the Mura-Zala Basin, and has been confirmed by hydrogeochemistry. The Újfalu (HU) and Mura (SLO) Formations are a part of the active regional thermal groundwater flow system, probably hydraulically separated from the shallower flow system of the Ptuj-Grad (SLO), Zagyva and Somló-Tihany (HU) Formations. The thermal water is of meteoric origin, reductive and alkaline. The predominant water type in the Quaternary and Pliocene aquifers is Ca–Mg–HCO3, changing to Na–HCO3 in the main Pannonian geothermal aquifer, and Na–Cl brine in deeper and older Miocene aquifers. Total dissolved solids and Na content generally increase with depth. Deuterium is in the range −87‰ to −75‰, 18O from −11.9‰ to −10.4‰, while 14C values are less than 6.1pmC in the samples of the active regional thermal groundwater flow system. These and results of noble gas analyses indicate recharge during the Pleistocene interglacial period with temperatures around 6–7°C. Regional thermal water resources are limited and environmental isotopes can be used as an early warning in the management of thermal water.