Tropical weathering has important linkages to global biogeochemistry and landscape evolution in the East African rift. We disentangle the influences of climate and terrestrial vegetation on chemical weathering intensity and erosion at Lake Malawi using a long sediment record. Fossil pollen, microcharcoal, particle size, and mineralogy data affirm that the detrital clays accumulating in deep water within the lake are controlled by feedbacks between climate and hinterland forest composition. Particle-size patterns are also best explained by vegetation, through feedbacks with lake levels, wildfires, and erosion. We develop a new source-to-sink framework that links lacustrine sedimentation to hinterland vegetation in tropical rifts. Our analysis suggests that climate-vegetation interactions and their coupling to weathering/erosion could threaten future food security and has implications for accurately predicting petroleum play elements in continental rift basins.