The supply of nutrients to the low-latitude thermocline is largely controlled by intermediate-depth waters formed at the surface in the high southern latitudes. Silicic acid is an essential macronutrient for diatoms, which are responsible for a significant portion of marine carbon export production. Changes in ocean circulation, such as those observed during the last deglaciation, would influence the nutrient composition of the thermocline and, therefore, the relative abundance of diatoms in the low latitudes. Here we present the first record of the silicic acid content of the Atlantic over the last glacial cycle. Our results show that at intermediate depths of the South Atlantic, the silicic acid concentration was the same at the Last Glacial Maximum (LGM) as it is today, overprinted by high silicic acid pulses that coincided with abrupt changes in ocean and atmospheric circulation during Heinrich Stadials and the Younger Dryas. We suggest these pulses were caused by changes in intermediate water formation resulting from shifts in the subpolar hydrological cycle, with fundamental implications for the nutrient supply to the Atlantic.