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Description: Large tropical sediment routing systems have relatively stable output fluxes over observable timescales. However, the functioning of sediment transfer in these systems across Pleistocene climate and sea-level fluctuations is not well documented. Here, we use new U-Pb detrital zircon (DZ) geochronology from the Pleistocene Amazon submarine fan (n=1,362 grains) to investigate provenance signatures through space and time in Earth’s largest source-to-sink system (~7x106 km2 onshore). DZ U-Pb ages from the Amazon River system display a progressive downstream dilution of Phanerozoic zircons by older cratonic zircons, predicting a submarine fan with significant proportions of craton-derived sediment. Rather than resembling DZ distributions of the lowest reaches of the Amazon, the well-mixed DZ signature of the Pleistocene submarine fan is nearly identical to an integrated Holocene Amazon system. We hypothesize that base level (sea level) is a first-order control on spatiotemporal patterns of DZ ages in the river and submarine fan: during higher sea level, the Amazon system experiences efficient sediment trapping in its lower reaches. During lower sea levels, the Amazon responds with incision and an increased gradient, resulting in reduced onshore to coastal sediment retention, channel lengthening, and enhanced throughput of Andean derived DZs to the deep sea. We speculate that this phenomenon may influence DZ compositions in other river to submarine fan systems globally.