Miocene strike-slip tectonics was responsible for creating and closing short-lived (ca. 6 Ma) passages and the emergence of isolated topography in the Northern Andes. These geological events likely influenced the migration and/or isolation of biological populations. To better understand the paleogeography of the Miocene hinterland and foreland regions in the Northern Andes, we conducted a source-to-sink approach in the Magdalena Basin. This basin is located between the Central and Eastern Cordilleras of Colombia and contains an ample Miocene record, which includes Lower Miocene fine-grained strata and Middle Miocene to Pliocene coarsening-up strata. Our study presents a new data set that includes detrital U–Pb zircon ages (15 samples), sandstone petrography (45 samples) and low-temperature thermochronology from the Southern Central Cordillera (19 dates); which together with previously published data were used to construct a paleogeographical model of the Miocene hinterland and foreland regions in the Northern Andes. The evolution of the Magdalena Basin during the Miocene was characterized by playa and permanent lake systems at ca. 17.5 Ma, which may be related to a marine incursion into NW South America and western Amazonia. The appearance of Eocene to Miocene volcanic sources in the Honda Group after ca. 16 Ma suggests the development of fluvial passages, which connected the Pacific with the western Amazonia and Caribbean regions. These passages were synchronous with a time of Miocene exhumation and topographic growth (ca. 16 to 10 Ma) in the Central Cordillera and the transition from lacustrine to fluvial deposition in the Magdalena Basin. Middle to Late Miocene strike-slip deformation promoted by oblique plate convergence and the oblique collision of the Panamá-Chocó Block likely explains the synchronous along-strike fragmentation and exhumation in the Central Cordillera.