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• First integrated seismic and fluid study of Czech Vienna Basin geothermal system. • Steinberg and Lanžhot-Hrušky faults control recharge–discharge fluid flow. • Identified Badenian and Sarmatian aquifers with geothermal potential. • Fluids show 3400–21,000 ppm TDS and inflow up to 14.5 m³/h. • Hydrocarbon data repurposed to advance low-temperature geothermal use. This study investigates the geothermal potential of the Czech sector of the Vienna Basin, a region traditionally explored for hydrocarbons, through the integration of seismic and fluid data. The analysis focuses on low-temperature geothermal systems (<150°C) hosted by Badenian and Sarmatian (Langhian–Serravallian) sedimentary sequences. Seismic interpretation identifies key structural features, including the Steinberg Fault Zone, serving as a recharge area, and the Lanžhot–Hrušky Fault Zone, representing a discharge area of a topography-driven geothermal fluid-flow system connected by a network of densely spaced aquifers. Hydrogeochemical analyses reveal total dissolved solids ranging from 3400 to 21,000 ppm and fluid inflow rates from 0.5 to 14.5 m³/h. Current limitations include incomplete data coverage and relatively low geothermal gradients; however, the availability of extensive hydrocarbon infrastructure and a large well database provides a unique opportunity for geothermal exploration and redevelopment. Deepening of selected wells in the most promising areas could increase reservoir temperatures, improving the economic efficiency of future geothermal projects. This study provides the first integrated structural and hydrogeothermal interpretation of the Czech sector of the Vienna Basin. The results identify a topography-driven geothermal circulation system controlled by the Steinberg and Lanžhot–Hrušky Fault Zones, linking recharge and discharge zones across multiple Badenian and Sarmatian aquifers. These findings establish a well-constrained conceptual framework for the basin’s geothermal system and demonstrate the potential for direct-use applications based on existing exploration data.