The subsurface Beetaloo Sub-basin of the McArthur Basin, Northern Territory, Australia, comprises a succession of shallow-water, dominantly marine, clastic sedimentary rocks that formed in the main depocentre of the Mesoproterozoic Roper Group. This group contains the oldest commercial hydrocarbons known, whose presence has been linked to changing nutrient flux controlled by a changing provenance. LA-ICP-MS detrital zircon U–Pb age data presented here provide new age constraints on the upper Roper Group and reveal spatial and temporal provenance variations illustrating the evolution of the basin and its margins that are linked to a major provenance change caused by the coeval collision of the combined South Australian Craton/North Australian Craton with the West Australian Craton.The maximum depositional ages of the Bessie Creek Sandstone and the Velkerri Formation of the Roper Group are constrained to 1386 ± 13 Ma and 1308 ± 41 Ma, respectively, whereas the overlying Moroak Sandstone has no younger detrital zircons, so its maximum depositional age is also constrained as 1308 ± 41 Ma. The Kyalla Formation was deposited after 1313 ± 47 Ma, and two, as yet, informally defined and ungrouped latest Mesoproterozoic to Neoproterozoic sedimentary units, the lower and upper Jamison sandstone, have maximum depositional ages of 1092 ± 16 Ma and 959 ± 18 Ma, respectively. Large detrital zircon age datasets (of 1204 near-concordant analyses) indicate that zircons from the Maiwok Subgroup were originally sourced from Palaeoproterozoic and earliest Mesoproterozoic rocks. These are consistent with derivation from the surrounding exposed basement. Detrital zircon age variations up-section suggest a systematic temporal change in provenance. The oldest formation analysed (Bessie Creek Sandstone) has a major source dated at ca. 1823 Ma. Rocks of this age are common in northern basement exposures. Samples from the overlying Velkerri Formation, show derivation from a ca. 1590 Ma source, consistent with rocks exposed in Queensland, or the Musgrave Province. The Moroak Sandstone and the Kyalla Formation show progressively more ca. 1740 Ma detritus, which we suggest likely reflects new sources in the Arunta Region to the south.We suggest that the provenance variation initially records exposure and denudation of western Queensland rocks at ca. 1400 Ma due to rifting between Laurentia and the North Australian Craton. From then until at least ca. 1320 Ma, the increased ca. 1740 Ma detritus suggests uplift of the Arunta Region that we interpret as reflecting collision between the southern North Australian Craton and the West Australian Craton as ca. 1300–1400 Ma. This tectonically-controlled provenance change is interpreted to have included erosion of nutrient rich arc-rocks that may have caused a bacterial bloom in the Roper Seaway. The Jamison sandstone and overlying Hayfield mudstone represent a marked change in provenance and were deposited after the Musgrave Orogeny, representing a newly-recognised siliciclastic basin that may have formed a shallow, long wavelength foreland basin to areas uplifted during the Musgrave Orogeny.