Thermal waters in Topusko (Croatia), with temperatures of up to 65 °C, have been used for heating, health, and recreational tourism for the past fifty years. Hydrogeochemical monitoring can provide insights into deeper geological processes and indicate system changes from baseline levels. It helps to identify potential anthropogenic impacts, as well as natural changes. Hydrogeochemical, geothermometrical, and environmental isotope studies of thermal waters in Topusko were conducted to improve the existing conceptual model of the Topusko hydrothermal system (THS), providing a baseline for continuous monitoring of the thermal resource. 2-year thermal springs and precipitation monitoring took place from March 2021 until March 2023. Major anions and cations, stable and radioactive isotopes (i.e. 18O, 2H, SO42−, 3H and 14C) and geothermometers were used to assess the origin of thermal waters in Topusko and their interaction with thermal aquifer. The results indicate the meteoric origin of thermal water, which was recharged in colder climatic conditions around the late Pleistocene–Early Holocene. Thermal water was last in contact with the atmosphere before approximately 9.5 kyr. Ca-HCO3 hydrochemical facies suggests carbonate dissolution as the dominant process driving the solute content. Geothermometrical results indicate an equilibrium temperature in the reservoir of 90 °C.