In tropical Africa, Late Pleistocene-Holocene climatic fluctuations heavily impacted the continental hydro-systems. The timing and magnitude of ‘African Humid Period’ hydrological dynamics (AHP; ~14.8 to ~5.5 ka BP) are not yet fully understood due to the extreme variability in African geomorphic patterns and the complex network of past air convergence boundary shifts. The investigation of the functioning of specific hydro-sedimentary basins is needed to improve our knowledge on the AHP spatial and chronological patterns over the continent. In this paper we present a revised Holocene lake level curve of Lake Abhe: an endorheic basin situated in the Afar Depression at the northern extremity of the East African Rift System (EARS). Located at the boundary of the Red Sea and the Indian and Atlantic Oceans’ air moisture mass fluxes, the Lake Abhe watershed represents a system sensitive to changes in Northeast African hydro-climate. Based on numerous littoral lacustrine geomorphic features and 53 related radiocarbon ages on stromatolites and nearshore deposits, we have defined the main Holocene lake highstands proposing a detailed paleo-shoreline record. The first rise in water level is dated to ~11.1 ka cal. BP, while the Maximal Holocene Highstand Shoreline (~420 m a.s.l.) was rapidly reached around ~10 ka cal. BP. Evidence of the impact of the 8.2 ka North Atlantic cooling event is recognized with slow lake level regression until ~8.3 ka cal. BP and with an abrupt drop at ~8 ka cal. BP. The resurgence of humid conditions was recorded from ~7.7 ka cal. BP to ~4.6 ka cal. BP. Radiocarbon ages on littoral materials allow us to propose a Holocene subsidence rate of the Abhe basin axial valley. Furthermore, multiphase sill overflow incisions towards the downstream Hanle basin and transient fluvial connectivity with the upstream Ziway-Shala basin, indicate strong geomorphic controls on lake highstand elevations. In summary, Lake Abhe Holocene fluctuations are the result of combined hydro-climatic, tectonic and local geomorphic controls. However, the confrontation with others East African basins allows us to discuss the transport of moisture masses dynamics into the northern EARS during the Holocene.