Abstract. Estuarine regions are generally considered a major source of atmospheric CO2, as a result of the high organic carbon (OC) mineralization rates in their water column and sediments. Despite this, the intensity of anaerobic respiration processes in the sediments tempered by the reoxidation of reduced metabolites near the sediment–water interface controls the flux of benthic alkalinity. This alkalinity may partially buffer metabolic CO2 generated by benthic OC respiration in sediments. Thus, sediments with high anaerobic respiration rates could contribute less to local acidification than previously thought. In this study, a benthic chamber was deployed in the Rhône River prodelta and the adjacent continental shelf (Gulf of Lion, northwestern Mediterranean) in late summer to assess the fluxes of total alkalinity (TA) and dissolved inorganic carbon (DIC) from the sediment. Concurrently, in situ O2 and pH micro-profiles, voltammetric profiles and pore water composition were measured in surface sediments to identify the main biogeochemical processes controlling the net production of alkalinity in these sediments. Benthic TA and DIC fluxes to the water column, ranging between 14 and 74 and 18 and 78 mmol m−2 d−1, respectively, were up to 8 times higher than dissolved oxygen uptake (DOU) rates (10.4±0.9 mmol m−2 d−1) close to the river mouth, but their intensity decreased offshore, as a result of the decline in OC inputs. In the zone close to the river mouth, pore water redox species indicated that TA and DIC were mainly produced by microbial sulfate and iron reduction. Despite the complete removal of sulfate from pore waters, dissolved sulfide concentrations were low and significant concentrations of FeS were found, indicating the precipitation and burial of iron sulfide minerals with an estimated burial flux of 12.5 mmol m−2 d−1 near the river mouth. By preventing reduced iron and sulfide reoxidation, the precipitation and burial of iron sulfide increases the alkalinity release from the sediments during the spring and summer months. Under these conditions, the sediment provides a net source of alkalinity to the bottom waters which mitigates the effect of the benthic DIC flux on the carbonate chemistry of coastal waters and weakens the partial pressure of CO2 increase in the bottom waters that would occur if only DIC was produced.