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This study aims to investigate the intricate relationship between geological structures, water chemistry, and isotopic composition in order to gain a deeper understanding of the origins and recharge mechanisms of thermal–mineral waters in the Kyllini region. The research integrates tectonic analysis, hydrochemical data, and stable isotope measurements to delineate recharge zones and trace the origin of these unique water sources. The methods used for delineation are the geological and tectonic study of the area, as well as hydrochemical and isotopic data analysis. The findings highlight that tectonic activity creates preferential flow paths and consequently influences the hydrogeological framework, facilitating deep circulation and the upwelling of thermal waters. Monthly analyses of groundwater samples from the Kyllini thermal spring were conducted over one hydrological year (2019–2020) and compared with data from the area collected in 2009. The hydrochemical profiles of major and minor ions reveal distinct signatures corresponding to various water–rock interactions, while stable isotope analysis provides insights into the climatic conditions and altitudes of recharge areas. Hydrochemical analyses reveal the composition of thermal–mineral waters, aiding in the identification of potential sources and their evolution. The conceptualization of Kyllini contributes to the deeper understanding of the intricate interplay between tectonics, hydrochemistry, and stable isotopes. During a hydrological year, the water type of Kyllini’s spring groundwater remains the same (Na-Cl-HCO₃), presenting only slight alterations. Full article