Between 14.5 and 5 ka, the Sahara was vegetated owing to a wet climate during the African humid period. However, the climatic factors sustaining the “green Sahara” are still a matter of debate. Particularly the role of winter precipitation is poorly understood. Using the stable hydrogen isotopic composition (δD, where D stands for deuterium) of high molecular weight (HMW) n-alkanoic acids in a marine sediment core from the eastern Mediterranean, we provide a continuous record for winter precipitation in the Nile river delta spanning the past 18 kyr. Pairing the data with δD records from HMW n-alkanes from the same core, we show that HMW n-alkanoic acids constantly derived from the delta, while the HMW n-alkanes also received significant contributions from the headwaters between ∼ 15–1 ka when fluvial runoff enhanced. This enables us to reconstruct the evolution of Mediterranean (winter) and monsoonal (summer) rainfall in the Nile river watershed in parallel. In the delta, the Heinrich stadial 1 (HS1) evolved in two phases, with a dry episode between ∼ 17.5–16.0 ka, followed by wet conditions between ∼ 16–14.5 ka. Winter rainfall enhanced substantially between 11–6 ka, lagging behind the intensification of the summer monsoon by ca. 3 kyr. Heavy winter rainfall resulted from a southern position of the Atlantic storm track combined with elevated sea surface temperatures in the eastern Mediterranean, reinforcing local cyclogenesis. We show that during the green Sahara, monsoon precipitation and Mediterranean winter rainfall were both enhanced and infer that the winter rainfall zone extended southwards, delivering moisture to the Sahara. Our findings corroborate recent hypotheses suggesting that winter rains that extended southward were a crucial addition to the northward displacement of the summer monsoon in helping to sustain a green Sahara.