Deep carbonate aquifer systems have been the target areas of geothermal investments. However, the scientific knowledge of groundwater flow, heat transport, and hypogene karstification processes is limited, which can cause significant risks in investments. The development and application of flow system theory for unconfined and confined half-basins led to a better understanding of influencing processes. We propose an adapted geological risk analysis methodology—first applied for deep carbonate aquifer systems—to be carried out before geothermal investments. The quantified probability of success can be a tool for making investment decisions through calculating the financial success and the cost of failure. Also they can be used when deciding on applications for funding, since projects can be ranked based on their POS, thus, the projects with the least geological and project risks can be funded first. The Buda Thermal Karst is a target of scientific and economic interest thanks to its unique geological and beneficial geothermal conditions. Our case study suggests favourable reservoir and thermal parameters, with moderate risk of aquifer quality, thermal conditions and injection-related risks. This study along with the background research on BTK supporting the geological risk assessment proves the potential of confined hypogene karsts for geothermal exploitation here and in similar deep karst areas.