This work describes the geochemical and hydrogeological characteristics of Santa Cesarea Terme, an active sulfuric acid speleogenetic system located along the Adriatic coastline (Apulia, southern Italy). It represents a very peculiar site, where rising thermal and acidic waters mix with seawater creating undersaturated solutions with respect to CaCO3, able to dissolve and corrode limestone and create caves. The Santa Cesarea Terme system is composed of four caves: Fetida, Sulfurea, Gattulla, and Solfatara. Hypogene morphologies and abundant deposits of native sulfur (especially in Gattulla Cave) and sulfate minerals are present in these caves. Fetida and Gattulla caves were investigated primarily because they are easily accessible throughout the whole year through artificial entrances, the other caves being reachable only from the sea. Geochemical analysis of water, monitoring of cave atmosphere, and measurement of the stable isotopes of S, O, and H helped to identify the main processes occurring in this complex cave system. In particular, changes in Ba2+ and Sr2+ concentration allowed for the identification of two main domains of influence, characterized by marine and rising acidic waters.