Host rock mechanical heterogeneities influence the spatial distribution of deformation structures and hence predictions of fault architecture and fluid flow. A critical factor, commonly overlooked, is how rock mechanical properties can vary over time, and how this will alter deformation processes and resultant structures. We present field data from an area in the Borborema Province, NE Brazil, that demonstrate how temporal changes in deformation conditions, and consequently processes, exert a primary control on the spatial distribution and geometric attributes of evolving deformation structures. Furthermore, each temporal deformation phase imparted different hydraulic architecture. The earliest flowing structures are localized upon subtle ductile heterogeneities. Following fault formation, both fault core and damage zone were flow conduits. In later stages of faulting pseudotachylyte welding created a low-permeability fault core and annealed high-permeability fractures within the fault damage zone. Modern flow occurs along a zone of later open shear fractures, defined by the mechanical strength contrast between the host rock and annealed fault. This second hydraulically conductive zone extends hundreds of metres from the edge of the annealed fault damage zone, creating a flow zone far wider than would be predicted using traditional fault scaling relationships. Our results demonstrate the importance of understanding successive deformation events for predicting the temporal and spatial evolution of hydraulically active fractures.