Study RegionPannonian Basin, Central and Eastern Europe. Study focusThis study, carried out by the geological surveys of Hungary, Slovenia, Austria and Slovakia, combines a joint characterization of a transboundary thermal groundwater system based on harmonised geological and hydrogeological data, with hydrodynamic modelling, delivering recommendations for authorities and policy makers on how they could improve the long term management of thermal groundwater. A porous, intergranular, multi-layered, Upper Pannonian aquifer system was the focus of this investigation. This deep sedimentary basin, up to 8000 m deep, has favourable conditions for geothermal exploitation, with centuries old thermal water usage and plans for increased utilization in all countries. New hydrological insights for the regionCross border areas with significant transboundary flow rates were identified, which have decreased due to thermal water production, with flow direction reversal across the Hungarian-Slovakian border. Thermal water production causes significant transboundary effects with depression cones that can penetrate several tens of kilometres into the neighbouring countries. Simulated drawdowns at the state borders are in the range of 2–10 m. Thermal water should therefore be exploited using doublets.Nine benchmark indicators (monitoring status, best available technology, thermal efficiency, utilisation efficiency, re-injection rate, quality of discharged thermal water, over-abstraction, status of water balance assessment, public awareness) were defined and tested at different transboundary regions and are demonstrated to be highly effective in groundwater management.