The southern Red Sea is a key region for investigating the effect of climate forces on a semi-closed basin. Detailed micropaleontological (planktic foraminifera) and isotopic (δ18Ο, δ13C) analyses along with reconstructions of sea surface temperature and salinity on a sediment core from the Farasan banks revealed the imprints of sea level changes and the South Asian Monsoon on the area. Comparison with surrounding records provided insights on the Red Sea-Gulf of Aden (GoA)-Northwestern Arabian Sea (NWArS) water exchange pattern over the last 30 ka. During glacial sea-level lowstand, flow of water from the GoA prevented hypersalinity in the southern Red Sea. Deglacial sea level rise improved water mass exchange between the NWArS, GoA and the entire Red Sea, resulting in relatively similar surface water conditions during the early Holocene when sea-level rise slowed. Thus, sea level change is the major driver of Red Sea δ18O variability. Southwest Monsoon (SWM), which was dominant during the late glacial and Early–Middle Holocene, enhanced surface productivity in the southern Red Sea. Northeast Monsoon (NEM) dominated around Heinrich stadial 1, as indicated by a nearly aplanktonic zone that was probably caused by restricted GoA inflow and low productivity.