Widespread drought characterized the Heinrich 1 and Younger Dryas cold periods of the last deglaciation throughout much of Africa, causing large increases in dust emissions from the Sahara and Sahel. At the same time, increases in wind strength may have also contributed to dust flux, making it difficult to interpret dust records alone as reflecting changes in rainfall over the region. The Niger River has the third largest drainage basin in Africa and drains most of the Sahara and Sahel and thus preserves and propagates climatic signals. Here, we present new reconstructions of Niger Delta sea surface salinity and Niger River discharge for the last 20,000 years in order to more accurately reconstruct the onset of the Western African Monsoon system. Based on calculated delta O-18(SEAWATER) (delta O-18(SW)) and measured Ba/Ca ratios in planktonic foraminifera, these new records reflect changes in sub-Saharan precipitation across the Niger River Basin in West Africa and reveal that the West African Monsoon system began to intensify several thousand years after the equatorial Monsoon system in Central Africa. We also present new records of primary productivity in the Niger Delta that are related to wind-driven upwelling and show that productivity is decoupled from changes in Niger River discharge. Our results suggest that wind strength, rather than changes in monsoon moisture, was the primary driver of dust emissions from the Sahara and Sahel across the last deglaciation.