Rapid tectonic uplift on the Alpine Fault, New Zealand, elevates topography, regional geothermal gradients, and the depth to the brittle ductile transition, and drives fluid flow that influences deformation and mineralisation within the orogen. Oxygen and hydrogen stable isotopes, fluid inclusion and Fourier Transform Infrared (FT-IR) analyses of quartz from veins which formed at a wide range of depths, temperatures and deformation regimes identify fluid sources and the depth of penetration of meteoric waters. Most veins formed under brittle conditions and with isotope signatures (δ18OH2O = −9.0 to +8.7‰VSMOW and δD=−73 to −45‰VSMOW) indicative of progressively rock-equilibrated meteoric waters. Two generations of quartz veins that post-date mylonitic foliation but endured further ductile deformation, and hence formation below the brittle to ductile transition zone (>6–8 km depth), preserve included hydrothermal fluids with δD values between −84 and −52‰, indicating formation from meteoric waters. FT-IR analyses of these veins show no evidence of structural hydrogen release, precluding this as a source of low δD values. In contrast, the oxygen isotopic signal of these fluids has almost completely equilibrated with host rocks (δ18OH2O = +2.3 to +8.7‰). These data show that meteoric waters dominate the fluid phase in the rocks, and there is no stable isotopic requirement for the presence of metamorphic fluids during the precipitation of ductilely deformed quartz veins. This requires the penetration during orogenesis of meteoric waters into and possibly below the brittle to ductile transition zone.