Detrital zircon U-Pb geochronology data from late Carboniferous to Triassic clastic sedimentary rocks in SW Iberia were used to investigate the regional paleogeography during the transition from Pangea amalgamation to break-up. The major U-Pb zircon age peaks are middle Devonian to Carboniferous (~390–300Ma), Cambrian-Ordovician (~530–440Ma), Cryogenian-Ediacaran (~750–540Ma), Stenian-Tonian (~1.2–0.9Ga) and Paleoproterozoic (~2.3–1.8Ga). Rapid exhumation of Variscan crystalline rocks at the contact between the South Portuguese zone and Ossa Morena Zone, explains the abundance of late Paleozoic ages in the upper Carboniferous-lower Permian continental successions. The U-Pb zircon data constrain the maximum depositional age of the Santa Susana Basin to c. 304Ma and the Viar Basin to c. 297Ma. The Triassic sequences, despite being c. 100Ma younger than the Variscan tectonothermal events, contain low proportions of late Paleozoic zircon. The major peaks in all zircon spectra closely resemble those found in the adjacent basement rocks, indicating small source areas, mainly located near the rift shoulders. Longer travelled fluvial systems are postulated for the eastern portions of the Algarve Basin, which was closer to the westward advancing Tethys Ocean than the rift basins of West Iberia. Sequences that contain significant proportions of ~1.2–0.9Ga zircon are probably recycled from post-collisional Carboniferous-Permian continental deposits that were more extensive than those found today.