Chemical weathering of silicate rocks on continents acts as a major sink for atmospheric carbon dioxide and has played an important role in the evolution of the Earth’s climate. However, the magnitude and the nature of the links between weathering and climate are still under debate. In particular, the timescale over which chemical weathering may respond to climate change is yet to be constrained at the continental scale. Here we reconstruct the relationships between rainfall and chemical weathering in northeast Africa for the last 32,000 years. Using lithium isotopes and other geochemical proxies in the clay-size fraction of a marine sediment core from the Eastern Mediterranean Sea, we show that chemical weathering in the Nile Basin fluctuated in parallel with the monsoon-related climatic evolution of northeast Africa. We also evidence strongly reduced mineral alteration during centennial-scale regional drought episodes. Our findings indicate that silicate weathering may respond as quickly as physical erosion to abrupt hydroclimate reorganization on continents. Consequently, we anticipate that the forthcoming hydrological disturbances predicted for northeast Africa may have a major impact on chemical weathering patterns and soil resources in this region.