A comprehensive hydrogeochemical survey of the geothermal waters from the Nappe Zone (Maghrebides fold-and-thrust belt) was undertaken to determine the origins of geothermal waters and to assess the health risks associated with their potentially toxic elements. A total of 11 geothermal water and 3 stream water samples were collected and analysed for major and trace elements (As, B, Ba, Fe, Mn, Pb, Sr, Zn). Two main geothermal water groups were highlighted by hydrogeochemical diagrams and multivariate analyses (PCA, HCA): the first group is the Na−Cl type, TDS > 10 g/L, controlled by deep circulation, while the second group is the Na-Cl−HCO₃ type, TDS < 2 g/L, and controlled by shallow circulation. A curved hydrogeochemical evolution path, observed from mixed bicarbonate shallow groundwater to chloride geothermal water, indicates that the interaction with evaporites drives the chemistry of the geothermal samples. On these, the As enrichments come from sulphide oxidation polymetallic mineralisation during the upwelling to the surface from E–W major lineaments. Therefore, E–W lineaments are potential areas for mineral prospecting. The health risk assessment reveals that the concentration of potentially toxic elements in geothermal waters are lower than the guideline values for the protection of freshwater aquatic life and dermal exposure (bathing or balneology).