Shelf anoxia and recurring sulphidic water column conditions are characteristic features of the coastal upwelling system off Namibia. The development of oxygen-depleted water column conditions is linked to the relative dominance of South Atlantic Central Water, which flows southward from the Angolan Dome over Eastern South Atlantic Central Water. Inter-and intra-annual variations in the strength of upwelling influence the thickness and stability of the relatively stagnant boundary layer. Hydrogen sulphide accumulation in this boundary layer is mainly driven by the diffusive flux of hydrogen sulphide from the sediment. The hydrogen sulphide derives from the rapid degradation of organic material by bacterial sulphate reduction in the topmost 20 cm of sediment. Low reactive iron contents in the diatomaceous mud belt limit iron sulphide precipitation and sulphide oxidation by oxidized iron. In the absence of oxygen, iron, and manganese as important electron acceptors, sulphide oxidation proceeds largely by the reduction of nitrate by the large sulphur bacteria Beggiatoa and Thiomargarita, which cover large areas of the shelf. Regional differences in the distribution of these bacteria affect the development of sulphidic bottom waters. While hydrogen sulphide is quantitatively oxidized in sediments covered by Beggiatoa mats, only a fraction of the sulphide is removed by Thiomargarita. Areal estimations of aerobic water column respiration, diffusive fluxes of hydrogen sulphide from the sediment, and rates of bacterial sulphate reduction indicate that oxidation of sulphide at the sediment-water interface and oxidation of water column sulphide may comprise up to 25 % of the total oxygen consumption in the coastal upwelling system. Advective transport of methane and hydrogen sulphide from gas-charged sediments has an intermittent and locally restricted impact on water column sulphide.