The Danube Deep-Sea Fan (NW Black Sea) is one of the most developed deep-sea sediment depositional systems in Europe. Although the morphology and the architecture have been widely described in the past years, little is known about the stratigraphy of this depositional system. For the late Quaternary, this results from the lack of significant stratigraphic markers, the scarcity of radiocarbon ages and the difficulty in constraining reservoir ages. Recent robust quantification of reservoir ages has allowed the construction of a new stratigraphic framework for the Black Sea from the end of the last glacial period to the Holocene, thus giving the opportunity to correlate sedimentological and geochemical features previously described on the NW Black Sea margin with climatic events identified in the Northern Hemisphere. Based on this approach, we propose an improved chrono-lithostratigraphic framework for the Danube Deep-Sea Fan channel–levees since the Last Glacial Maximum. We show that the Danube Deep-Sea Fan was active during the Last Glacial Maximum until the Younger Dryas–Early Holocene transition ca. 11,700 cal a. BP, when the turbidite activity abruptly terminated in the whole system. Throughout this period, the Danube River was the main source of the deep depositional system, except between ca. 17,200 cal a. BP and 15,700 ± 300 cal a. BP. At that time, the deposition of ‘red turbidites’ in the deep basin, concomitant with the deposition of the so-called ‘Red Layers’ onto the continental shelf and the upper slope, emphasises the direct impact of the increased meltwater runoff of the Dnieper River as far as the Danube Deep-Sea Fan. Some significant changes in the location of the depocentre of the Danube Deep-Sea Fan occurred through time. The main change in depocentre location occurred at ca. 28,000 cal a. BP, with the northward avulsion leading to the formation of the Middle Channel. Although the Middle and Northern Channel became the preferential turbidite depocentres after this event, the deposition of turbidites has persisted in the Southern channel–levee until 14,700 cal a. BP, indicating that the Southern Channel was definitely not abandoned after the upstream northward avulsion. Unsurprisingly, water-level fluctuations and river sediment flux acted as the main forcings on the evolution of the Danube Deep-Sea Fan. Based on these results, and on the morphology of the Danube Canyon, we propose that (i) lowstand conditions (≤ − 110 m) prevailed during the Last Glacial Maximum, and possibly between 15,700 ± 300 cal a. BP and 14,700 cal a. BP, (ii) water-level ranged from ≥ − 110 and ≤ − 70 m between 14,700 and 11,700 cal a. BP, and (iii) water-level ranged from ≥ − 70 and ≤ − 30 m from 11,700 cal a. BP and until the reconnection of the Black Sea ‘Lake’ with the global ocean at ca. 9000 cal a. BP.