The present-day Middle Magdalena Valley, Eastern Cordillera, and Llanos Basin were once part of a large, multiphase basin system that began as an extensional basin during the Late Triassic–Early Jurassic and evolved into a retroarc foreland basin by the Late Cretaceous. By the late Eocene, this system was segmented into hinterland and foreland basins. Although the tectonostratigraphic evolution of these transitions is well understood, the basin architecture during each phase has not been fully reconstructed. In this study, we integrate stratigraphic and chronostratigraphic data from these basins and adjacent areas to develop a comprehensive regional framework. This correlation enabled the identification and mapping of Late Campanian and Maastrichtian maximum flooding surfaces, associated with the back-arc and retroarc foreland basin stages. Tracing these surfaces from the Llanos Basin to the Middle Magdalena Valley allows reconstruction of the basin’s spatial configuration through each tectonic phase. Our results document how basin architecture evolved in response to northeastward orogenic loading and the development of intrabasin structural highs, which led to localized erosion and non-deposition during the Campanian–Maastrichtian. These insights are critical for predicting the distribution and preservation of Lower Cretaceous marine deposits, which represent significant hydrocarbon source rocks. Additionally, we assess whether Maastrichtian sediment load and burial conditions were sufficient to trigger hydrocarbon generation in these source units, using the maximum flooding surfaces as chronostratigraphic markers.