Modern Lake Chad has shrunk in area by around 90 % since the 1960s under the twin pressures of climate change and increasing water demand. During the early to mid Holocene, the Chad basin featured a megalake with an area approximately 100 times larger than its modern remnant. In the mid/late Holocene (approximately 5000 years ago), this megalake dried out leaving behind vast deposits of readily deflated fine-grained sediments that are suggested to contribute ∼25 % of the annual total global atmospheric mineral dust load. Erosion has obliterated much of the evidence of earlier North African humid periods within the Lake Chad basin, limiting our understanding of the relationship between global/regional climatology, local hydrology and dust export. Here, we present new records of thorium-normalized flux estimates of mineral dust and its radiogenic isotope composition deposited at Ocean Drilling Program Site 662, situated downwind of Megalake Chad underneath the North African winter dust plume, in the equatorial Atlantic Ocean. Our records show that sediments of the Megalake Chad basin have a distinct neodymium isotopic signature that can be traced thousands of kilometers downwind from their source when the megalake basin was dry and dust-active, whereas the fingerprint of its input was strongly suppressed at times of high lake levels. Our results show that marine sedimentary archives can preserve uninterrupted proxy records of climate-driven hydrological change on the continents, in this case, a bellwether region of Africa that features the world's most active dust source, the Bodélé Depression. • We present radiogenic isotope compositions of five North African dust source areas. • Megalake Chad sediments have a distinctive isotopic fingerprint. • Dust supply to Eq. Atlantic Ocean driven by Chad basin rainfall/hydrology. • ODP662 provides continuous records of endorheic Lake Chad inundation/desiccation. • Comparison of dust fluxes and isotopes reveals impact of wind and tropical rainbelt.