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The exploration of the geothermal potential of a geological unit has multiple aspects. The most important elements are the geological structure, the hydrogeological conditions, and heat flow. The analysis of the above-mentioned elements attempts to help maximize the use of a geothermal aquifer’s potential. When choosing the most appropriate geophysical method, it is important to consider various factors, such as basic structural parameters as well as the total cost of exploration. This is especially true for low-thermal areas. Comparison of multi-geophysical exploration methods used in the study of the carbonate aquifer of the Humenné Unit identified the advantages and weaknesses of each method. The Humenné Unit is the north basement unit of the Eastern Slovak Basin (with a heat flow value ranging from 100 to 125 mW·m−2), which is part of the Pannonian Basin (with a high heat flow ranging from 50 to 130 mW·m−2). The calculation of the geothermal potential was based on the results of several methods. Some important geophysical survey methods resulted in: (a) deep seismic cross-sections which clarified the position and overall internal structure of the aquifer (b) gravimetric measurements in the form of a map of the Complete Bouguer Anomalies (calculated for density 2.67 g·cm−3) which confirmed the presence of structural elevations and depressions. These elevations and depressions intensified the water yield, heat flow and raised the overall temperature (c) the use of geoelectric resistivity profiling, which is a fast and cheap method, but is limited by depth. The similar resistivities ρ: 80–360 Ωm of carbonates and andesites was a serious problem. The specific heat-energy potential has a wide range of 0.337–19.533 GJ/m2. The highest values above 15 GJ/m2 are reached in areas where the temperature on the surface of the Triassic carbonates exceeds 90 °C.