The geothermal resource is one of the great sources of energy on the planet. The conventional prospecting of this type of energy is a slow process that requires a great amount of time and significant investments. Nowadays, geophysical techniques have experienced an important evolution due to the irruption of UAVs, which combined with infrared sensors can provide great contributions in this field. The novelty of this technology involves the lack of tested methodologies for their implementation in this type of activities. The research developed is focused on the proposal of a methodology for the exploration of hydrothermal resources in an easy, economic, and rapid way. The combination of photogrammetry techniques with visual and thermal images taken with UAVs allows the generation of temperature maps or thermal orthomosaics, which analyzed with GIS tools permit the quasi-automatic identification of zones of potential geothermal interest along rivers or lakes. The proposed methodology has been applied to a case study in La Hermida (Cantabria, Spain), where it has allowed the identification of an effluent with temperatures close to 40 °C, according to the verification measurements performed on the geothermal interest area. These results allow validation of the potential of the method, which is strongly influenced by the particular characteristics of the study area.