Fluids play a key role in modifying the chemical and physical properties of fault zones, which may prime them for repeated rupture by the generation of high pore fluid pressures and precipitation of commonly weak, secondary minerals. Fluid flow paths, sources and fluxes, and the permeability evolution of fault zones throughout their seismic cycles remain poorly constrained, despite their importance to understanding fault zone behaviour. Here we use geochemical tracers of fluid-rock exchange to determine budgets for meteoric, metamorphic and mantle fluids on a major compressional tectonic plate boundary.The Alpine Fault marks the transpressional Pacific-Australian plate boundary through South Island, New Zealand and appears to fail in regular (329±68 yrs) large earthquakes (Mw∼8) with the most recent event in 1717 AD. Significant convergent motion has formed the Southern Alps and elevated geothermal gradients in the hangingwall, which drive crustal fluid flow. Along the Alpine Fault the Alpine Schist of the Pacific Plate is thrust over radiogenic metasedimentary rocks on the Australian plate. The absence of highly radiogenic (87Sr/86Sr > 0.7200) strontium isotope ratios of hangingwall hot springs and hydrothermal minerals formed at a range of depths in the Alpine Fault damage zone indicates that the fluid flow is restricted to the hangingwall by a cross-fault fluid flow barrier throughout the seismogenic crust. Helium isotope ratios measured in hot springs near to the Alpine Fault (0.15-0.81 RA) indicate the fault is a crustal-scale feature that acts as a conduit for fluids from the mantle. Rock-exchanged oxygen, but meteoric water-like hydrogen isotope signatures of hydrothermal veins indicate that partially rock-exchanged meteoric fluids dominate down to the top of the brittle to ductile transition zone at ∼6 km. Geochemical tracer transport modelling suggests only ∼0.02 to 0.05% of total rainfall west of the Main Divide penetrates to depth, yet this recharge flux is sufficient to overwhelm other fluid contributions. Calculated mantle fluid fluxes of CO2 and H2O (0.2 and 3 to 13 mol/m2/yr respectively) and metamorphic H2O fluxes (4 to 750 mol/m2/yr) are considerably lower than the focused meteoric water discharge flux up the Alpine Fault (4 × 103 to 7 × 104 mol/m2/yr), driven by the >3000 m hydrologic head of the Southern Alps. Meteoric waters are primarily responsible for modifying fault zone permeability during fluid-rock interactions and may facilitate the generation of high pore fluid pressures that could assist episodic earthquake rupture.