Topusko is the second warmest natural thermal water spring area in Croatia, located at the southwest edge of the Pannonian Basin System. Due to favourable geothermal properties, these waters have been used for heating and health and recreational tourism since the 1980s. Thermal springs with temperatures up to 50 °C are the final part of an intermediate-scale hydrothermal system. However, systematic research on the Topusko spring area has not been conducted to lay the foundation for sustainable resource utilisation. Multidisciplinary research including the hydrogeochemical characterisation of naturally emerging thermal water, an electrical resistivity tomography (ERT) investigation conducted to reconstruct the subsurface geology, and hydrogeological parametrisation of the geothermal aquifer was carried out to refine the existing local conceptual model. The results show Ca-HCO3 facies of Topusko thermal waters, which get heated in a Mesozoic carbonate aquifer. The water equilibrium temperature in the geothermal aquifer is estimated to be 78 °C based on the SiO2-quartz geothermometer. The fault damage zone, which enables the upwelling of thermal water, was identified by ERT investigations. The transmissivity values of the aquifer derived from the results of step-drawdown tests range from 1.8 × 10−2 to 2.3 × 10−2 m2/s. Further multidisciplinary research is necessary to improve the existing conceptual model of the Topusko hydrothermal system.