A hydrochemical and mineral study of groundwaters and damaged rocks from the Tíscar and Larva fault zones (Betic Cordillera, Iberian Peninsula) was carried out in order to (a) describe the physical and chemical properties of the groundwaters; (b) recognize significant locations with deep-origin fluids related to active tectonics; (c) and to describe the water–rock interaction and the neoformation of clay mineral processes and their importance in the seismicity of the faults. A sampling campaign was completed between November 2012 and November 2013, during which data were obtained from 23 different groundwater sites in the fault areas. Two main groups of waters were distinguished: (a) Ca2+-Mg2+-HCO3− facies characterized by poor conductivity and salinity; and (b) saline waters (up to 30 meq/L) rich in Ca2+-Mg2+-SO4-Cl− and with an elevated conductivity (frequently > 1000 μS/cm). In addition, a minor group of saline and warm waters (T > 16.5 °C) was found to be Na+-rich and show moderately high B values (>0.33 ppm), and which mig ht be hosted in aquifers deeper than the two main groups. This group of deep-origin waters is oversaturated in clay minerals and is in equilibrium for Ca-Mg carbonate minerals. X-ray diffraction and scanning and transmission electron microscopy data corroborate the crystallization forecast of authigenic smectite, which appears as thin films coating carbonate fragments. The origin of smectite is related to the fragile strain and thermal–fluid–mineral interactions in fault rocks. Smectite could lubricate carbonate rocks, which favor creep deformation versus seismic slip. This work provides locations where groundwater physico-chemical properties and composition suggest tectonic fault activity.