Data from two cross-shelf sediment sampling cruises were used to explain reasons for the sediment biogeochemical variability in respect of carbon, nitrogen and sulphur, and how the cycling of these elements governs the biogeochemistry of the overlying water through their control of the redox conditions. The spatial extent of this benthic-pelagic flux link is limited to the innershelf mud belt system on the Namibian shelf. The inshore mud belt is the primary deposition area of the carbon and nitrogen new production export flux. The offshore organic-rich zones are thought to be relict particulate organic matter originating from the inshore mud belt rather than from an overlying pelagic source. These data were used to set up a multi-layer sediment model that was used through sensitivity analyses to elucidate the input characteristics that result in the most significant feedbacks on hypoxia in the overlying water. The analyses showed that, although the new production flux is a requirement to drive an oxygen demand in the sediments, the onset and persistence of anoxia may depend critically on a low-oxygen boundary condition threshold. Keywords: anoxia, Benguela Current, carbon, hypoxia, modelling, Namibia, sediment biogeochemistry.