High-resolution records of sea surface temperatures (SSTs) and terrestrial n-alkanes (TERR-alkanes) combined with pollen from the same sedimentary sequences were generated to assess variations in the Nile River discharge over the Holocene. These independent proxy records indicate a period of wetter conditions in the Nile watershed during the early-Holocene consistent with insolation-driven enhanced monsoon precipitation, known as the African Humid Period (AHP). The detection of a dry episode around 9200 yr BP in the TERR-alkane and pollen time series suggests a temporary weakening of the monsoon intensity most probably triggered by extratropical cooling in the North Atlantic. An interval of C4 grass expansion between 8800 and 8400 yr BP was also evidenced from the TERR-alkane distribution and confirmed by palynological data. SSTs of the coastal waters off the Nile delta reveal strong fluctuations in the early-Holocene followed by a slight warming and two pronounced cold intervals around 3500 yr BP and 1500 yr BP. Comparison of these results with the same proxy data acquired from the Rhone River sediments (NW Mediterranean Sea) highlights an east–west contrast in the climate signals.