In addition to ocean acidification due to a gradual anthropogenic CO2 uptake, strong seasonal variations in the carbonate system occur in the Arctic Ocean as a result of physical and biological processes. Understanding this seasonal variability is critical for predicting the onset of calcium carbonate mineral (Ω) undersaturation with increasing atmospheric CO2 concentrations. However, these variations are currently poorly understood because of a lack of winter data due to the challenging field conditions in this season. Here we report observations over an annual cycle of the carbonate system of surface waters in the Atlantic gateway to the Arctic Ocean, covering the region between Svalbard and mainland Norway. Dissolved inorganic carbon (DIC) concentrations ranged from 2137–2148 μmol kg− 1 in winter to 1986–2094 μmol kg− 1 in summer, and total alkalinity (TA) concentrations between 2312–2341 μmol kg− 1 in winter and 2199–2317 μmol kg− 1 in summer. This resulted in an increase in TA:DIC ratios from 1.077–1.090 in winter to 1.106–1.112 in summer, mainly due to the biological uptake of CO2 during spring and summer. Similarly, a significant seasonal variability was observed in Ω (0.4–0.9), with lowest saturation states in winter (Ωaragonite ~ 1.8–2.1) and highest in spring and summer (Ωaragonite ≈ 2.4). Analysis of the biogeochemical and physical processes that impact aragonite saturation states (Ωar) showed biological production to be the most important factor driving seasonal variability in Ωar in this area, accounting for 45–70% of the difference between winter and summer values. Future changes in these processes may alter the seasonal cycle of the carbonate system in both amplitude and timing, and further observations are required to determine the progress of ocean acidification in the Atlantic waters entering the Arctic Ocean.