Springs have an important role both in groundwater flow system understanding and in maintaining groundwater-related ecosystems. The aim of the research of the lukewarm karst springs in Kistapolca is to understand the origin of the elevated temperature (22–24 °C), i.e., whether it is the result of mixing of cold and thermal waters or it represents the terminal area of intermediate flow systems. This question has also an important relevance to the evaluation of recent cave formation in the area. In case of mixing of different waters dissolution by mixing corrosion could take place. This scenario was proposed for the formation of the Beremend Cave, which is situated in the close vicinity of the springs, and which is the only known cave of the area, where the passages are partly filled by water. Therefore, several methods, including geophysical, geochemical and stable isotope measurements, evaluation of continuous-time series of water level change, temperature, and electrical conductivity data and hydraulic evaluation of vertical flow conditions by pressure–elevation profiles were combined in order to acquire information about the hydrogeological environment and flow conditions in the area. The results show that a higher order flow system derived from the Villány Hills feeds the springs in Kistapolca without significant local influence. In addition, the results related to the Beremend Cave indicate that cave formation by mixing corrosion is not an active process today in the area, the cave is rather influenced by local processes.