The carbonate chemistry of Arctic Ocean seafloor and its vulnerability to ocean acidification remains poorly explored. This limits our ability to quantify how biogeochemical processes and bottom water conditions shape sedimentary carbonate chemistry, and to predict how climate change may affect such biogeochemical processes at the Arctic Ocean seafloor. Here, we employ an integrated model assessment that explicitly resolves benthic pH and carbonate chemistry along a S—N transect in the Barents Sea. We identify the main drivers of observed carbonate dynamics and estimate benthic fluxes of dissolved inorganic carbon and alkalinity to the Arctic Ocean. We explore how bottom water conditions and in-situ organic matter degradation shape these processes and show that organic matter transformation strongly impacts pH and carbonate saturation (Ω) variations. Aerobic organic matter degradation drives a negative pH shift (pH < 7.6) in the upper 2—5 cm, producing Ω < 1. This causes shallow carbonate dissolution, buffering porewater pH to around 8.0. Organic matter degradation via metal oxide (Mn/Fe) reduction pathways further increases pH and carbonate saturation state. At the northern stations, where Ω > 5 at around 10–25 cm, model simulations result in authigenic carbonate precipitation. Furthermore, benthic fluxes of dissolved inorganic carbon (12.5—59.5 µmol cm−2 yr−1) and alkalinity (11.3—63.2 µmol cm−2 yr−1) are 2—3-fold greater in the northern sites due to greater carbonate dissolution. Our assessment is of significant relevance to predict how changes in the Arctic Ocean may shift carbon burial and pH buffering into the next century.