The Aysen region, located in Southern Patagonia, Chile (43°38′S to 49°16′S) has optimum conditions for the formation of geothermal systems: Magmatic processes, abundant rainfall and active faults systems. In fact, several thermal springs emerge in coastal and inland areas of the Aysen region. Thermal springs in the coastal areas are spatially related to the Liquiñe-Ofqui Fault System (LOFS), a major strike-slip fault system that runs along the southern segment of the Southern Volcanic Zone, and could be controlling groundwater circulation. Despite the existence of literature regarding the composition of thermal springs, they do not elucidate the origin of thermal waters, the source of their chemical components nor have their hydrogeochemical processes been investigated. This knowledge will provide a useful tool for exploration of geothermal resources in the Aysen region.Sixteen thermal waters, three fjord waters, and three meteoric water samples were collected and analysed for major-minor ions, some trace elements (B, Li) and stable isotopes of δ2H and δ18O. Classic geochemical tools (i.e.: ratio of elements, ion vs chloride content), Hierarchical Cluster Analysis (HCA) and Factorial Analysis (FA) suggest there are three water groups (G1, G2 and G3). G1 and G3 are NaCl type coastal thermal springs with electrical conductivity (EC) above 1000μS/cm and mostly neutral pH (6.4 to 8.4). G1 has the highest average concentrations of Cl−, SO42−, Na+, Ca2+ while G3 has the highest values T°, SiO2, HCO3−, Li, B. The G2 samples are from Aysen inland areas, have EC below 1000μS/cm, slightly alkaline pH (7.9 to 9.6) and are Na-Cl-HCO3 type with higher average values of T°, SiO2, HCO3− and Li than G1.Factorial analysis indicates that two factors explain 82.1% of the total dataset variance. Factor 1 is formed by Cl−, SO42−, Na+, Ca2+, Li and B, which we associated with fjord water mixing processes. The factor 2 formed by T°, SiO2, HCO3−, Li and B might be interpreted as: i) silicate weathering from the North Patagonian Batholith and ii) volatile elements transported through high temperature vapours from a volcanic degassing source. These two components which could interact and overlap are address as “magmatic-hydrothermal” in this work. The factorial scores distribution is consistent with the HCA suggesting that fjord water mixing is the dominant geochemical process for G1 samples while G2 samples are influenced by magmatic-hydrothermal fluids. The G3 thermal waters show both processes with a greater influence of magmatic-hydrothermal fluids. The calculated saline factor (3.4% to 42.3%) supports fjord water mixing processes as one of the dominant processes affecting the coastal thermal spring's composition.The stable isotopic data (δ2H and δ18O) fall in the local meteoric water line (LMWL), suggesting current recharge and limited oxygen isotopic exchange during rock-dissolution processes. This could indicate short residence times and/or abundant contribution of actual meteoric water at shallow depths.