We investigated one kastencore and multicores taken from the rapidly accumulating diatomaceous muds on the Namibian shelf to trace decadal-scale fluctuations of coastal upwelling by sedimentological, isotopic, geochemical, and paleo ecological methods. One specific objective was to reconstruct the fluctuations of fish populations (indicative of oceanographic and ecological conditions) using the occurrence of fish scales in varved sediment layers and to correlate these fluctuations with paleo environmental conditions. The partly laminated core was dated by 14C AMS and subsampled at high resolution (1 cm intervals), yielding a resolution of about 3–10 years per sample. The interval for which data are available covers the last 3200 years. The core contains scales of all fish species which are associated with a typical upwelling community: sardines, anchovies, mackerel, jack mackerel, hake and myctophids. Accumulation rates of organic matter and fish scales fluctuated considerably. The variability in abundance and type of fish scales at different depths indicates drastic fluctuations of fish abundance in the Benguela Current during the last 3200 years, as well as changes in community structures. The paleo environmental conditions associated with the different phases of fish population abundance are reflected in the frequency of laminations (indicative of anoxic conditions on the shelf), and by variations of stable isotopes of organic matter. The δ15N-signature of fish scales from surface sediments shows a 15N-enrichment of 6‰ related to the average sedimentary δ15N composition. This indicates that pelagic fish diet was a mixture of 20% algae to 80% zooplankton. We postulate fish scale δ15N preserves information of the relative nitrate consumption of algae in the upwelling system without any diagenetic imprints. This investigation might become a contribution to the discussion of diagenesis in the δ15N-signature of bulk sediments.