The drainage integration of three Late Pleistocene intramontane basins located in the southern Italian Apennines was reconstructed by integrating information derived from geomorphic, structural, and stratigraphic analyses. The Santaloja (SLJ), Lago (LG), and Pantani (PN) basins are located in the axial zone of the Apennines fold-and-thrust belt where they mainly comprise Mesozoic to Cenozoic deep-sea water siliceous and calcareous rocks. The Quaternary development of these intramontane basins draining the Basento River catchment provides an example of drainage evolution within collisional mountain belts and its tectonic and climatic controlling mechanisms. Tectonically, sets of NW-SE- and NE-SW-trending faults formed a large trough with ensuing river valley development configured to synclinal folds. The ongoing interplay of these active and passive tectonic controls lead to compartmentalisation into three endorheic basins. Uncalibrated radiocarbon dating of peat layers from boreholes reveals that lacustrine facies conditions prevailed during the Late Pleistocene, spanning 34,785 to 41,325 ka during Marine Isotope Stage 3. Morphometric analysis suggests that these endorheic lacustrine basins subsequently became integrated via overspill from 13.25 kyr calBC onwards linked to Late Pleistocene climatic changes creating the Basento River. Within the axial zone of the southern Apennines, tectonically driven headwards erosion is commonly attributed to lengthening of major rivers like the Basento River. However, this study demonstrates a more complex interplay between tectonics and climate change for intramontane basin development and its drainage evolution.