Generic models of continental-margin evolution predict that siliciclastic fluxes to slopes should be maximal and minimal during major sea-level lowstands and transgressions, respectively. Here we document the opposite for the northeast Australian margin, the largest extant mixed siliciclastic-carbonate depositional system. Cores from slopes of this margin consistently contain siliciclastic-rich intervals, ∼0.3–1 m thick, in the upper few meters. Radiocarbon dates of planktonic foraminifera show that this interval was deposited between 12 and 7 ka and represents greatly increased siliciclastic fluxes during late transgression. This massive terrigenous discharge to slopes occurred along at least 450 km of the margin, irrespective of modern variations in bathymetry or climate. Although we cannot dismiss a significantly different early Holocene climate with greatly enhanced sediment discharge, available data instead suggest that rivers aggraded on the shelf during lowstand because of an extensive subaerially exposed reef system. This phenomenon may occur on other margins rimmed by reefs, requiring a major revision of concepts used to interpret mixed siliciclastic-carbonate systems.