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The Archaean to Mesoproterozoic basement of northern South Australia is almost completely overlain by thick Neoproterozoic and younger basins (<< 1% outcrop), yet is likely to preserve an important record of the interactions between the Archean-Proterozoic Gawler Craton and the Proterozoic Musgrave Province during the amalgamation of Australia in the Proterozoic. However, constraints on the location and geometry of the boundary between these provinces are poor. We use potential field data to determine the 3D basement architecture and so constrain where this Palaeo-Mesoproterozoic boundary may be located beneath the Eastern Officer Basin. We establish the geometry and properties of the overlying basins and explicitly include them during forward and inverse modelling of potential field data to highlight the structure of the underlying basement. Our analysis identifies three crustal domains. (1) Southeast of the steep northeast-southwest Middle Bore Fault, positive gravity and magnetic anomalies are co-located and sourced from bodies in the upper crust, these bodies overlie middle to lower crust that is apparently uniform. (2) Between the Middle Bore Fault and the southern edge of the Munyarai Trough, the highest amplitude gravity and magnetic anomalies are not co-located and are sourced from large northwest dipping bodies. (3) To the northwest, the crust underlying the Munyarai Trough has similar properties to the Musgrave Province, suggesting that the Musgrave Province extends at least 50 km beneath the Eastern Officer Basin. Although details of the geology in the second (central) domain are poorly constrained, the domain preserves large crustal-scale Precambrian structures and is interpreted to mark the boundary between the Gawler Craton and the Musgrave Province. In particular, the multiply reactivated Middle Bore Fault forms a major crustal boundary and is interpreted to mark the northern limit of the Gawler Craton. The Middle Bore Fault may have formed as early as the Kimban Orogeny (similar to 1.7 Ga), although substantial reactivation and modification of the crustal architecture could have occurred between the Kimban Orogeny and intrusion of the cross-cutting Gairdner Dolerite Dykes (827 Ma). Refereed/Peer-reviewed