Detrital zircon U-Pb geochronology has been used extensively to develop provenance histories for surface outcrops of key stratigraphic localities within sedimentary basins. However, many basins lack sufficiently continuous and widespread exposures of complete successions to evaluate proposed long-term tectonic histories, stratigraphic correlations, and paleodrainage patterns within individual basins. Here, we demonstrate the utility of subsurface detrital zircon U-Pb analysis by integrating ages from three key wells (21 subsurface samples) with previously reported data from six exposed intervals (90 surface samples) within a single basin. Samples from the 5–10-km-thick clastic successions span several structural blocks over an ∼300 × 50 km swath of the Middle Magdalena Valley Basin, a north-trending intermontane basin in the northern Andes of Colombia. Available U-Pb age distributions for modern rivers highlight the distinctive signatures of several competing sediment sources, including two major contiguous ranges (Central Cordillera and Eastern Cordillera) and two localized block uplifts (Santander Massif and San Lucas range). U-Pb results from Jurassic through Neogene stratigraphic units spanning the nine surface and subsurface sites, including several type localities, enable comparisons of provenance shifts at specific sites and spatial variations among key stratigraphic intervals across multiple sites.