The Blue Nile is the major contributor of freshwater and sediments to the modern-day main Nile River and exerts a key control on seasonal flooding in the Nile valley. Recent studies have postulated that the relative contribution from the Blue Nile to the main Nile runoff might have been reduced during the mid-Holocene, at a time when higher boreal summer insolation stimulated enhanced precipitation in North Africa. Whether the decrease in the relative contribution from the Blue Nile resulted from a decrease in precipitation over the catchment, from an increase in White Nile runoff or from a combination of both is still a matter of debate. By comparing regional proxy-records with the output from a global atmospheric model zoomed on Africa, we propose that the reduced contribution from the Blue Nile at 6 ka originated from both a higher White Nile runoff and a lower Blue Nile runoff. Enhanced African and Indian monsoons at 6 ka induced a northern shift of the Intertropical Convergence Zone and an eastward shift of the Congo Air Boundary. Such an atmospheric configuration led to a negative anomaly of summer precipitation over the Blue Nile catchment that likely resulted in a reduction in the Blue Nile runoff. By contrast, a sustained positive anomaly of precipitation over the White Nile catchment during both summer and autumn most likely induced a higher main Nile runoff during the mid-Holocene. Using the model output, we propose a first synoptic view on regional rainfall dynamics that permits to reconcile contrasting proxy records.