Here we present evidence that the Holocene African monsoon system (AMS) varied in response to the eastern equatorial Atlantic sea-surface temperature (SST). Several short-term episodes of decreased moisture availability as a result of low eastern equatorial Atlantic SST are suggested by planktonic foraminiferal Mg/Ca ratios. These episodes promoted a weakening of the AMS and thus determined the timing and intensity of arid periods. Local sea-surface salinities also reveal regional patterns of precipitation in equatorial western Africa. The high eastern equatorial Atlantic SSTs occur in concert with seasonally increased insolation at low latitudes, suggesting a strong response of African monsoonal precipitation to oceanic conditions at low latitudes.