The c. 1.5–1.3 Ga Wilton package, the upper succession of the greater McArthur Basin, preserves detailed tectono-sedimentary evidence for the Mesoproterozoic evolution of the North Australian Craton (NAC). In addition, it is a valuable global sedimentary repository for the poorly explored Mesoproterozoic. New detrital zircon U–Pb age and Lu–Hf isotope data, collected from multiple, geographically separated, basins that make up the Wilton package, are compiled with previously published data to illuminate the basin evolution. The spatial and temporal variation in sedimentary provenance illustrates two major geographic changes that correspond to continent-scale tectonic convulsions of the NAC during the Mesoproterozoic. The first is shown by the influx of sediment sourced from east and southeast terranes. This is linked to rifting between Proterozoic Australia and Laurentia at c. 1.45 Ga, resulting in the uplift of the eastern margin of the NAC–SAC (South Australian Craton). The second basin geographic change is illustrated by a flux of southerly-sourced detritus that is interpreted to be tectonically driven by the uplift of the southern NAC, during the subduction/closure of the Mirning Ocean at c. 1.32 Ga. Spatially, sediment in the Wilton package is separated into two depositional systems: sedimentary rocks within the Birrindudu Basin, the western component of the Wilton package, have different detrital signatures relative to other Wilton package successions found east of the Daly Waters Fault Zone, in the Beetaloo Sub-basin, the McArthur Basin and the South Nicholson Basin. The Daly Waters Fault Zone is interpreted as an ancient bathymetric high, blocking sediment transport. Although they differ in sources, rocks in both the Birrindudu Basin and the eastern Wilton package record coeval shifts of basin provenance to southern sources. The coherent evolution of basin provenance indicates a consistent tectono-sedimentation history, and links the Birrindudu Basin and the other Wilton successions in a tectonic framework.