The Permo-Carboniferous glacial Dwyka Group deposits in Namibia provide the first evidence for high sedimentation rates caused by a Carboniferous/Permian extensional stress regime in southern Gondwana, which eventually led to the opening of the southern Atlantic Ocean in the Early Cretaceous. Besides palaeocurrent direction measurements, the use of U–Th–Pb data in combination with morphometrics of detrital and magmatic zircons is a not well studied approach to determine fluxes and reworking processes of glacial and marine clastic sediments. Roundness values of 7–8 for the investigated zircon grains are very common, suggesting long transport distances and/or multiple recycling. In addition, abundant scratches and collision marks indicate high energy environments during transport. Only one ash bed and one sandstone sample featured low roundness values and smooth zircon surfaces, indicating low transport energies. Zircon ages from all concordant analyses can be clustered into several groups: Cryogenian to early Cambrian (c. 0.7–0.5 Ga; 15%), major early Neoproterozoic to late Mesoproterozoic (c. 0.95–1.25 Ga; 46%), late (1.9–1.7 Ga; 8%) as well as a middle Palaeoproterozoic (2.1–1.9 Ga; 5%) and scarce Archaean (3%). The first age group may be confined to Pan-African magmatic events occurring around the Kalahari Craton margin, whereas the protosource of Mesoproterozoic ages may be the Namaqua Metamorphic Complex. Palaeoproterozoic structural units folded in the course of the Namaqua Orogeny as well as the late Palaeoproterozoic Rehoboth Belt, are possible source areas for the Palaeoproterozoic ages. The youngest zircons from an ash bed were dated at 296.2 ± 2.3 Ma and suggest an Asselian age for the upper Zwartbas Formation (DS II), pointing to a duration of 12 Ma for DS II-IV, assuming a duration of 3–6 Ma for the three uppermost glacio-eustatic cycles. The data suggests that the siliciclastic successions of the Dwyka Group mainly consist of reworked material, with minor input of freshly eroded material. An initial diamictite deposit, possibly induced by a southerly directed ice advance, occurring in the southern part of the Aranos Basin, recycled parts of the Nama Basin fill and covered the latter strata based on the difference in zircon age spectra. All subsequent deglaciation sequences indicate prevalent westward ice movement. A recycling of the detrital zircon grains over several generations is also implied by an increase in mean zircon width/length ratio and width as a function of age. The Permian evolution of southern Gondwana was confined by the occurrence of pre-Dwyka erosional plains and deep glacial scoured valleys reaching into its interior, which were successively covered by extensively recycled material of various protosources and consequently eroded by the Dwyka aged tillites.