On Quaternary time scales, the global biogeochemical cycle of silicon is interlocked with the carbon cycle through biotic enhancement of silicate weathering and uptake of dissolved silica by vascular plants and aquatic microalgae (notably diatoms, for which Si is an essential nutrient). Large tropical river systems dominate the export of Si from the continents to the oceans. Here, we investigate variations in Si cycling in the upper White Nile basin over the last 15 ka, using sediment cores from Lakes Victoria and Edward. Coupled measurements of stable O and Si isotopes on diatom separates were used to reconstruct past changes in lake hydrology and Si cycling, while the abundances of lipid biomarkers characteristic of terrestrial/emergent higher plants, submerged/floating aquatic macrophytes and freshwater algae document past ecosystem changes. During the late-glacial to mid-Holocene, 15–5.5 ka BP, orbital forcing greatly enhanced monsoon rainfall, forest cover and chemical weathering. Riverine inputs of dissolved silica from the lake catchments exceeded aquatic demand and may also have had lower Si-isotope values. Since 5.5 ka BP, increasingly dry climates and more open vegetation, reinforced by the spread of agricultural cropland over the last 3–4 ka, have reduced dissolved silica inputs into the lakes. Centennial-to millennial-scale dry episodes are also evident in the isotopic records and merit further investigation.