The study of radiolarian assemblages from Core MD 962086 provides new information on the variability in the upwelling intensity and origin of upwelled water masses over the past 350 ky in one of the major filamentous regions of the Benguela Upwelling System (BUS), located off Lüderitz, Namibia. The use of key radiolarian species to trace the source of upwelled waters, and the use of a radiolarian-based upwelling index (URI) to reconstruct the upwelling intensity represent the first use of radiolarians for paleoceanographic reconstructions in the BUS. These radiolarian-based proxies indicate strongest upwelling during Marine Isotope Stages (MIS) 3, 5, and 8, which compares well with other studies. While during MIS 3 and 8, the radiolarian-based proxies indicate the influx of waters of Southern Ocean origin, they also point to the increased influence of tropical waters during the lower portion of MIS 5. During MIS 2, 4 and 6 the radiolarian assemblages indicate generally lower upwelling intensities, although this signal is complicated by the increased occurrence of organic carbon in the sediments during these intervals. During MIS 2 there appears to be less of an input of Southern Ocean waters to the BUS, although during the also glacial MIS 4 and 6, there is evidence for an increased influence of cold Antarctic waters. The comparison of the results from Core MD 962086 with other studies in the BUS area indicates a non-uniform pattern of upwelling intensity and advection of cold, southern waters into this system during MIS 2. Weaker upwelling signaled by the radiolarian-based proxy in MIS 4 is in contrast to other studies that indicate higher productivity during this time period. In general, the data show that there is a strong spatiotemporal complexity in upwelling intensity in the BUS and that the advection of water into it is not strongly tied to glacial–interglacial variations in climate.