Sequential nutrient regeneration and organic matter (OM) degradation in surface sediments of the Gulf of Trieste (northern Adriatic Sea) were examined using in situ benthic chambers under normoxic, anoxic and reoxic conditions. Intensive NH4+ and PO4− anoxic regeneration was subsequently slower in prolonged anoxia. NH4+ production was probably also a consequence of dissimilatory nitrate reduction to NH4+. The presence of anammox and laterally pumping of oxygenated water by benthic infauna explained the presence of NO3− in anoxia. Anoxic phases were characterized by enhanced dissolution of Sibiog, decreasing pore water Ca and Mg concentrations indicating carbonate precipitation and higher Fe and Mn concentrations as a result of reduction/respiration. Reoxygenation was characterized by enhanced bioturbation. Nitrification caused NH4+ decrease and P precipitated quickly as carbonate fluorapatite and FePO4. In addition adsorption of P onto Fe-hydroxides could also occur since Fe (and Mn) reoxidized quickly. Increased Ca levels suggested enhanced carbonate dissolution. Diffusive fluxes at the sediment–water interface (SWI), calculated from pore water modelling using diffusion-reaction model, revealed high anoxic NH4+ effluxes and Ca (and Mg) influxes. PO4− fluxes were very low and high NH4+/PO4− flux ratios in anoxic and reoxic phases suggested an excess of benthic inorganic N. Nutrient budgets at the SWI showed intensive anoxic recycling of inorganic N but low P and Si cycling in all redox phases.