The 5 km deep drilling at Soultz-sous-Forêts samples a granitic intrusion under its sedimentary cover. Core samples at different depths allow study of the evolving conditions of fluid-rock interaction, from the syntectonic emplacement of Hercynian granites at depth until post-cooling history and alteration close to the surface. Hydrogen, carbon and oxygen isotope compositions of CO2 and H2O have been measured in fluid inclusions trapped in magmatic quartz within samples collected along the drill core. Early Fluid Inclusions Assemblage (FIA) contains aqueous carbonic fluids whereas the latest FIA are H2O-rich. In the early FIA, the amount of CO2 and the δ13C value both decrease with depth, revealing two distinct sources of carbon, one likely derived from sedimentary carbonates (δ13C=−2‰V-PDB) and another fromthe continental crust (δ13C=−9‰V-PDB). The carbon isotope composition of bulk granites indicates a third carbon source of organic derivation (δ13C=−20‰V-PDB). Using a δD - δ18O plot, we argue that the water trapped in quartz grains is mainly of meteoric origin somewhat mixed with magmatic water. The emplacement of the Soultz-sous-Forêts granite pluton occurred in a North 030–040° wrench zone. After consolidation of the granite mush at ~600 °C, sinistral shear (γ ~ 1) concentrated the final leucocratic melt in vertical planes oriented along (σ1, σ2). Crystallization of this residual leucocratic melt occurred while shearing was still active. At a temperature of ~550 °C, crystallization ended with the formation of vertical quartz veins spaced about 5 mm, and exhibiting a width of several cm. The quartz veins form a connected network of a few kilometers in height, generated during hydrothermal contraction of the intrusion. Quartz crystallization led to the exsolution of 30% by volumeof the aqueous fluid. As quartz grainswere the latest solid phase still plastic, shearing localized inside the connected quartz network. Aqueous fluid was thus concentrated in these vertical channels. Eventually, when the channels intersected the top of the crack network, water boiling caused the formation of primary inclusions. At the same temperature, the saline magmaticwaters,which were denser than the meteoricwaters, initiated thermohaline convection with the buoyant “cold” hydrothermal water layer. This mechanismcan explain the mixing of surface and deep-seated fluids in the same primary inclusions trapped during the crystallization of magmatic minerals. This study, which separately considers fluid-rock interactions at the level of successive mineral facies, brings new insights into how fluids may be different, their origin and composition, and depending on tectono-thermal conditions, bears implications for eventual ore forming processes.