Based on a high-resolution analysis of the diatom signal and biogenic bulk components at site GeoB3606-1 (25°S, off Namibia), we describe rapid palaeoceanographic changes in the Benguela Upwelling System (BUS) from early MIS 3 through to the early Holocene (55 000 to 7 000 14C yr BP). Coastal upwelling strongly varied at 25°S from MIS 3 through to MIS 2. The abrupt decrease in the accumulation rate of biogenic silica and diatoms from MIS 3 into MIS 2 records rapid oceanographic changes in the BUS off Namibia. During MIS 3, leakage of excess H4SiO4 acid from the Southern Ocean into low-latitude surface waters, as indicated by the occurrence of Antarctic diatoms, enhanced the production of spores of Chaetoceros at the expense of calcareous phytoplankton. Furthermore, shallower Antarctic Intermediate Water (AAIW) would have enriched the thermocline off Namibia with silicate transported from the Southern Ocean. The strong decrease of the siliceous signal throughout MIS 2 represents a decrease in the nutrient input to the BUS, even though the diatom assemblage is still dominated by spores of the upwelling-associated diatom genus Chaetoceros. Depletion of silicate in the thermocline from the onset of MIS 2 through to the early Holocene reflects the shutdown of AAIW injection from the Southern Ocean into the BUS, causing upwelled waters to become reduced in silicate, hence less favourable for diatom production. The deglaciation and early Holocene are characterised by the replacement of the upwelling-associated flora by a non-upwelling-related diatom community, reflecting weakened upwelling, retraction of the seaward extension of the chlorophyll filament off Lüderitz, and dominance of warmer waters. Copyright © 2003 John Wiley & Sons, Ltd.