Comprehensive understanding of hydrothermal systems is often obtained through the integration of conceptual and numerical modelling. This integrated approach provides a structured framework for the reconstruction and quantification of fluid dynamics in the reservoir, thereby facilitating informed decision-making for sustainable utilisation and environmental protection of the hydrothermal system. In this study, an updated conceptual model of the Topusko hydrothermal system (THS; central Croatia) is proposed based on structural, geochemical, and hydrogeological analyses. The stratigraphic sequence and the structural framework of the THS were defined based on geological maps and field investigations. As depicted by hydrochemical and isotope analyses, thermal waters in Topusko (temperatures of up to 65 °C) are of meteoric origin and circulate in a carbonate aquifer. The THS receives diffuse recharge approximately 13 km S from Topusko, where Triassic carbonates crop out. Gravity-driven regional groundwater circulation is favoured by regional thrusts that tectonically uplifted Palaeozoic low permeable rocks. These structures confine the fluid flow in the permeable, fractured and karstified, Triassic carbonates favouring the northward circulation of the water. A regional anticline lifts the aquifer closer to the surface in Topusko. Open fractures in the anticline hinge zone increase the fracturing and permeability field of the aquifer promoting the quick upwelling of the thermal water resulting in the Topusko thermal springs. Numerical simulations of fluid flow and heat transport corroborate the proposed conceptual model. In particular, a thermal anomaly was modelled in the Topusko subsurface with temperature values of 31.3 °C and 59.5 °C at the surface and at the base of the thermal aquifer, respectively, approaching the field observations. These findings showed that the circulation of Topusko thermal water is influenced by regional and local geological structures suggesting that the enhanced permeability field in the discharge area enables the formation of the natural thermal springs.