Our prognostic model reproduces observed oxygen distribution and its variability. Benthic sulphur bacteria control sediment-water nutrient and oxygen fluxes. Zooplankton respiration is a major oxygen sink in the Namibian shelf water. Vertical migrating zooplankton introduces new time scales in oxygen dynamics. Zooplankton response to low oxygen may prevent anoxic shelf waters off Namibia. The organic mud belt makes the northern BUS an oxygen source to the atmosphere.