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Description: The Colorado River in the southwestern U.S. provides an excellent natural laboratory for studying the origins of a continent-scale river system, because deposits that formed prior to and during river initiation are well exposed in the lower river valley and nearby basinal sink. This paper presents a synthesis of regional stratigraphy, sedimentology, and micropaleontology from the southern Bouse Formation and similar-age deposits in the western Salton Trough, which we use to interpret processes that controlled the birth and early evolution of the Colorado River. The southern Bouse Formation is divided into three laterally persistent members: basal carbonate, siliciclastic, and upper bioclastic members. Basal carbonate accumulated in a tide-dominated marine embayment during a rise of relative sea level between ~6.3 and 5.4 Ma, prior to arrival of the Colorado River. The transition to green claystone records initial rapid influx of river water and its distal clay wash load into the subtidal marine embayment at ~5.4–5.3 Ma. This was followed by rapid southward progradation of the Colorado River delta, establishment of the earliest through-flowing river, and deposition of river-derived turbidites in the western Salton Trough (Wind Caves paleocanyon) between ~5.3 and 5.1 Ma. Early delta progradation was followed by regional shut-down of river sand output between ~5.1 and 4.8 Ma that resulted in deposition of marine clay in the Salton Trough, retreat of the delta, and re-flooding of the lower river valley by shallow marine water that deposited the Bouse upper bioclastic member. Resumption of sediment discharge at ~4.8 Ma drove massive progradation of fluvial-deltaic deposits back down the river valley into the northern Gulf and Salton Trough. These results provide evidence for a discontinuous, start-stop-start history of sand output during initiation of the Colorado River that is not predicted by existing models for this system. The underlying controls on punctuated sediment discharge are assessed by comparing the depositional chronology to the record of global sea-level change. The lower Colorado River Valley and Salton Trough experienced marine transgression during a gradual fall in global sea level between ~6.3 and 5.5 Ma, implicating tectonic subsidence as the main driver of latest Miocene relative sea-level rise. A major fall of global sea level at 5.3Ma outpaced subsidence and drove regional delta progradation, earliest flushing of Colorado River sand into the northern Gulf of California, and erosion of Bouse basal carbonate and siliciclastic members. The lower Colorado River valley was re-flooded by shallow marine waters during smaller changes in global sea level ~ 5.1–4.8 Ma, after the river first ran through it, which requires a mechanism to stop delivery of sand to the lower river valley. We propose that tectonically controlled subsidence along the lower Colorado River, upstream of the southern Bouse study area, temporarily trapped sediment and stopped delivery of sand to the lower river valley and northern Gulf of California for ~200–300 kyr. Massive progradation of the fluvial-deltaic system back down the river valley into the Salton Trough starting ~4.8–4.5Ma apparently was driven by a huge increase in sediment discharge that overwhelmed the sediment-storage capacity of sub-basins along the lower river corridor and established the fully integrated river channel network.