AbstractBiogeochemical cycles of carbon, nutrients, and oxygen transmit mean states, trends and variations of the physical realm in coastal upwelling systems to their food webs and determine their role in regional budgets of greenhouse gases. This contribution focuses on biogeochemical processes in the northern Benguela Upwelling System (NBUS), where low oxygen levels in upwelling source water are a major influence on carbon and nutrient cycles. Based on measurements during numerous expeditions and results of 3-D regional ecosystem modeling (project GENUS; Geochemistry and Ecology of the Namibian Upwelling System) we here examine source water character, effects of low oxygen conditions on nutrient masses and ratios, and of diazotrophic N2-fixation on productivity of the system and its transition to the adjacent eastern South Atlantic. In available observations, the effects of denitrification in water and sediment and phosphate release from sediments are minor influences on nitrate:phosphate ratios of the system, and excess phosphate in aged upwelling water is inherited from upwelling source water. Contrary to expectation and model results, the low N:P ratios do not trigger diazotrophic N2-fixation in the fringes of the upwelling system, possibly due to a lack of seeding populations of Trichodesmium. We also examine the flux of carbon from the sea surface to either sediment, the adjacent sub-thermocline ocean, or to regenerated nutrients and CO2. Observed fluxes out of the surface mixed layer are significantly below modeled fluxes, and suggest that regeneration of nutrients and CO2 is unusually intense in the mixed layer. This contributes to very high fluxes of CO2 from the ocean to the regional atmosphere, which is not compensated for by N2-fixation. Based on observations, the NBUS thus is a significant net CO2 source (estimated at 14.8 Tg C a− 1), whereas the CO2 balance is closed by N2-fixation in the model. Methane concentrations were low in surface waters in on-line measurements during 1 expedition, and based on these our estimate for the emission of methane for the entire Benguela system is below 0.2 Tg CH4 a− 1.