Reconstruction of nutrient concentrations in the deep Southern Ocean has produced conflicting results. The cadmium/calcium (Cd/Ca) data set suggests little change in nutrient concentrations during the last glacial period, whereas the carbon isotope data set suggests that nutrient concentrations were higher. We determined the silicon isotope composition of sponge spicules from the Atlantic and Pacific sectors of the Southern Ocean and found higher silicic acid concentrations in the Pacific sector during the last glacial period. We propose that this increase results from changes in the stoichiometric uptake of silicic acid relative to nitrate and phosphate by diatoms, thus facilitating a redistribution of nutrients across the Pacific and Southern Oceans. Our results are consistent with the global Cd/Ca data set and support the silicic acid leakage hypothesis.