This paper presents the results of an extensive chemical and isotopic investigation on natural thermal and cold fluids (spring waters and associated gases) discharging throughout the main geological domains of Morocco. The chemical features of the thermal springs are mainly dependent on rock dissolution involving Triassic evaporite formations, producing either Na–Cl or Ca–S0₄composition, although mixing with shallower connate high-saline waters in Neogene post-orogenic sedimentary layers cannot be ruled out. Only in the Moroccan Meseta and Anti-Atlas domains have spring discharges probably undergone equilibration as a result of water-rock interaction in granites. Of the chemical and isotopic features of the gas seeps,³He/⁴He ratios and δ¹³C–C0₂values indicate the occurrence of a significant contribution of mantle-derived gas, especially at Oulmès (Moroccan Meseta) and Tinejdad-Erfoud (Anti -Atlas), where associated waters are found to equilibrate at relatively high temperatures (c. 130 °C). These areas are also characterized by the presence of Pliocene to Quaternary basaltic volcanic rocks. Thermal discharges located along the Rif front and related to the NE–SW-oriented main strike-slip faults are associated with a CH₄- and/or N₂-rich gas phase, derived respectively from a crustal or an atmospheric source. Some of them have significant contents of ³He that could indicate the rising of mantle fluids. Such a striking isotopic signature, which is not related to any recent volcanism visible at surface, is likely to be associated with cooling magma at depth related to transpressive fault systems. Similarly, in the northeastern area, the small, although significant, enrichment of ³He in the gas discharges seeping out along the Nekor seismic active fault and related to Pliocene-Quaternary basalts also suggests a deep-seated (magmatic) contribution. The distribution of thermal discharges is strongly related to the main active tectonic structures of Morocco. Moreover, this study indicates the presence of deep active tectonic structures in areas until now considered as stable. In particular, the NE–SW-trending Nekor fault may be part of a major system that extends to the Moroccan Meseta and into the Smaala–Oulmés fault system, thus emerging as a deep structure with crustal significance.