The coastal upwelling system offshore Namibia is ideally suited to address a focal question of the Integrated Marine Biogeochemistry and Ecosystem Research Programme: what are the mechanisms that drive long-term changes in ecosystems? Considerable interannual variability in climatic forcing is indicated by long time series of meteorological and remote sensing observation; these accompany considerable interannual to interdecadal changes in the upwelling intensity over the last 100 years, as well as a centennial trend. On longer time scales, the only archives available are sediment records spanning the late Holocene. To decipher the sediment record, we mapped surface-sediment patterns of proxies for physical (sea surface temperature/SST from alkenone unsaturation indexes) and nutrient (d 15 N on bulk sedimentary N) variables. Their present-day surface-sediment patterns outline the coastal upwelling cells and filaments and associated high productivity area. Analysed in an array of dated sediment cores, the spatial patterns of SST suggest long-term ([100 years) variability in the location and intensity of individual upwelling cells. The patterns of d 15 N outline an area of intense denitrification near the coast, and advection of water with low-oxygen concentrations in the undercurrent from the North. d 15 N exhibits considerable downcore variability, in particular over the last 50 years. The variability appears to be governed by differences in extent of denitrification and thus of the shelf oxygen balance, which appears to have deteriorated in the last 50 years. Together, the data suggest that SST and denitrification conditions have remained in the narrow bounds outlined by today's patterns in surface sediments, but that spatially small variability in upwelling intensity and make-up of upwelling feed waters induced considerable changes in the lower trophic levels of the coastal upwelling ecosystem over the last 6,000 years. Attempts to correlate proxy records from sediments with observational time series and regional climate reconstructions were not successful, possibly because annual to interannual environmental signals are erased in the process of sediment formation.