The South Rif Thrust (Northern Morocco) is characterized by several thermo-mineral water sources with outlet temperatures ranging from 24 °C to 54 °C. The anomalous temperatures of these resurgences are linked to deep circulation in areas where the geothermal gradients are abnormally high (>35 °C km−1). Nonetheless, the factors that govern the geological environment, heat flux and chemical characteristics of these thermo-mineral waters are still poorly defined. In order to provide a more comprehensive knowledge of their potential as geothermal resources, a multidisciplinary geological, hydrogeochemical, and isotopic study was carried out in 2014.The results show a hydrochemical heterogeneity displaying a large range of chemical facies, salinity and outlet temperatures, attributed not only to water-rock interactions but as well to different degrees of mixing processes between water types (regional deep diluted waters, shallow cold immature waters and deep thermal waters). The isotopic signature of thermo-mineral waters sampled (δ18O, δ2H and 3H) suggests a similar meteoric origin, recharged before the 1950’s, but from two different recharge areas: (1) the pre-Rif, the Western Meseta and/or the South Rif Thrust itself and (2) the Meseta-Atlas domain. Theoretical equilibrium temperatures at depth, ranging from 50 to 150 °C, confirm their potential as geothermal resources and the computed reservoir depths (between 0.7 and 3.0 km) which also suggest a deeper groundwater circulation than those proposed by previous studies which considered the Mesozoic aquifer (∼1.5 km depth) as the main source.Finally, the spatial correlation between thermo-mineral springs resurgences at the intersection between E-W Rif thrusts and NE-SW strike-slip fault systems, highlights the importance of those geological structures as preferential paths for groundwater circulation, privileging those intersections as priority sites to conduct further geothermal exploration.