We assessed tectonic controls on the spatial and temporal distribution of fault zone flow pathways in the Rio Grande rift (New Mexico, USA) by using fault zone calcite cements as a geochemical record of syntectonic fluid flow. Cement δ18O, δ13C, and 87Sr/86Sr values indicate that older, large-displacement master and basin-margin faults were cemented by more isotopically evolved basinal brines than younger intrabasin faults. These data suggest that diagenetic fluids in basin-bounding faults equilibrated predominantly with downdip Paleozoic carbonates. In contrast, intrabasin faults transmitted fluids from shallow stratigraphic sources. This pattern of flow pathways is linked to the systematic distribution of sediments and faults that record rift evolution, which dictated spatial and temporal variations in fault zone architecture and permeability structure. Our results indicate that the depths from which fluids can be transported in active rift basins ultimately depend on both tectonically mediated variations in the grain size of syntectonic sediments entrained in fault damage zones and fault displacement magnitude.