The northern Namibian Karoo-aged successions are part of a Gondwana-wide sedimentary system emerging at the Carboniferous–Permian boundary and existing for more than 50 Ma. The Karoo Supergroup sedimentary successions are of importance in understanding the evolution of the Karoo rift system. This study presents new whole-rock geochemical data combined with detrital zircon morphology as well as U−Pb ages and Lu−Hf composition of late Palaeozoic siliciclastic rocks of the Namibian Huab Basin and Kunene area (south-west Africa). Inferred by youngest detrital zircon U−Pb ages the Verbrande Berg Formation (lower Ecca Group) yields a Sakmarian to Asselian maximum depositional age, whereas the overlying Tsarabis Formation yields an Artinskian maximum depositional age. These ages coincide with the end of the Dwyka ice age and an overall warming and a contemporaneous evolution of the Karoo I rift system across southern Gondwana. The zircon age distribution of the investigated samples yields clusters ranging between ca 500 to 650 Ma (Cambrian–late Neoproterozoic), ca 950 to 1200 Ma (early Neoproterozoic–Mesoproterozoic) and ca 1800 to 1900 Ma (Palaeoproterozoic). Their rounded shapes characterize the zircon grains of the Kunene area and the lower Huab Basin section, whereas upper Huab Basin strata yield mostly unrounded grains. The rounded nature of zircon grains with a diverse U−Pb age spectrum putatively points towards sediment homogenization and multiple recycling stages during the deposition of the sediments and large catchment areas of the depositing rivers. As suggested by zircon grains with a low roundness value and a single Palaeoproterozoic age cluster, the upper Huab Basin successions were probably deposited under drier climatic conditions, small catchment areas and limited sedimentary homogenization. Therefore, the southern Gondwana sedimentary transport and homogenization system may change over time and is dependent on the climate prevailing during deposition. This study shows that the laws of detrital zircon are very complex and are yet to be explored.