Intermontane basins are illuminating stratigraphic archives of deformation, denudation, and environmental conditions within the heart of actively growing mountain ranges. Commonly, however, it is difficult to determine from the sedimentary record of an individual basin whether basin formation, aggradation, and dissection were controlled primarily by climatic, tectonic, or lithological changes and whether these drivers were local or regional in nature. By comparing the onset of deposition, sediment-accumulation rates, incision, deformation, changes in fluvial connectivity, and sediment provenance in two interrelated intermontane basins, we can identify diverse controls on basin evolution. This work focuses on the Humahuaca basin and the Casa Grande basin, two adjacent intermontane basins currently connected by a bedrock gorge through the Sierra Alta, in the Eastern Cordillera of NW Argentina at ∼23-24°S. We combine detailed geologic mapping, stratigraphic analysis of measured sections, provenance data, and geochronology to reconstruct the history of deformation, deposition, basin isolation, and incision in these basins. The exceptional time control provided by U-Pb geochronology of numerous volcanic ashes contained within the Neogene-Quaternary basin fill combined with an unambiguous magnetostratigraphic record in the Humahuaca basin enables the comparison of multiple types of datasets, e.g., sediment-accumulation rates, timing of deformation on individual faults, detrital zircon provenance, paleocurrents ,and sedimentary facies, from both basins to discriminate between potential controls on specific events in each basin's history.