Prominent preexisting structural heterogeneities within the lithosphere may localize or partition deformation during tectonic events. The NE‐trending Great South Basin, offshore New Zealand, formed perpendicular to a series of underlying crustal terranes, including the dominantly granitic Median Batholith Zone, which along with the boundaries between individual terranes exert a strong control on rift physiography and kinematics. We find that the crustal‐to‐lithospheric scale southern terrane boundary of the Median Batholith Zone is associated with a crustal‐scale shear zone that was reactivated during Late Cretaceous extension between Zealandia and Australia. This reactivated terrane boundary is oriented at a high angle to the faults defining the Great South Basin. We identify a large granitic laccolith along the southern margin of the Median Batholith, expressed as subhorizontal packages of reflectivity and acoustically transparent areas on seismic reflection data. The presence of this strong granitic body inhibits the lateral southwestward propagation of NE‐trending faults, which segment into a series of splays that rotate to align along the margin as they approach. Further, we also identify two E‐W‐ and NE‐SW‐oriented basement fabrics, likely corresponding to prominent foliations, which are exploited by small‐scale faults across the basin. We show that different mechanisms of structural inheritance are able to operate simultaneously, and somewhat independently, within rift systems at different scales of observation. The presence of structural heterogeneities across all scales needs to be incorporated into our understanding of the structural evolution of complex rift systems.