The external or internal origin of CO2 and H2O in marbles and metabasites from a large-scale granulite section is related to their structural setting: outside shear zones, within major shear zones (≈ 25 km wide by >340 km long), or within minor shear zones (<10 km wide by <150 km long). Outside shear zones, marbles have isotopic compositions similar to their protholiths values and metabasites record mantle δ13C signatures. Marbles from major shear zones show little variation of δ18O but are depleted in 13C down to −3‰ due to exchange with mantle-derived carbon. In addition to an earlier input of mantle carbon related to mafic magmatism, major shear zones act as conduits for mantle carbon influx. They are probably mantle rooted. Oxygen was buffered by the crust. Marbles and their related skarns from minor shear zones were subjected to devolatilization reactions and water-rich infiltration from crustal sources with no evidence for a mantle carbon contribution. Large isotopic variations at the metre scale in the shear zones reflect the heterogeneous distribution of fluid flow associated with heterogeneous deformation and contrasting petrologic features and permeabilities. These geochemical-structural relationships reconcile the conflicting arguments on the origin of fluids during granulite genesis.