Production of biogenic silica and dissolution processes in the water column and surface sediment are important aspects for the investigation and reconstruction of present and past productivity of the ocean. Although the geological record of biogenic silica is often used as a proxy for paleoceanographic processes in the Southern Ocean, little is known about the present regional distribution of biogenic silica flux and accumulation and their relation to primary production in surface waters. Based on more than 130 sediment and pore water samples, the regional differences of the biogenic silica flux to the sea floor of the southern South Atlantic were investigated. In contrast to biogenic silica content, the dissolved Si-flux through the sediment/water interface, caused by intense dissolution of BSi in surface sediments, reflects biogenic production in surface waters. This was inferred by observed increases of Si-fluxes in regions of recurrent polynya formation or in the vicinity of Marginal Ice Zones as at the Weddell-Scotia Sea boundary. In the Scotia sea, where no benthic fluxes were reported before, we found a considerable burial of biogenic silica and biogenic silica fluxes to the sea floor of ~ 800-1300 mmol m-2a-1. This is a significantly higher flux than derived for the known opal accumulation area in the SE Atlantic, further to the east in the Antarctic Circumpolar Current, where a flux of ~ 600-767 mmol m-2 a-1 was observed. This shows that the Scotia Sea is not a gap within the Circumpolar Antarctic Opal Belt as previously assumed. The geochemical budget for different sub-regions of the South Atlantic was considered by a Geographic Information System. In contrast to most previous attempts, this ensures the accurate consideration of the spatial distribution of sampling sites, a crucial aspect for the accuracy of geochemical budgets. For the South Atlantic we calculated the flux of biogenic silica to the sea floor as ~5.1 x 1012 mol a-1. Only ~ 0.84 X 1012 mol a-1 is buried in these sediments, which is considerably less than previous estimates.