Abstract. The temporal variation of the carbonate system, air–sea CO2 fluxes, and pH is analyzed in the southern Indian Ocean, south of the polar front, based on in situ data obtained from 1985 to 2021 at a fixed station (50°40′ S–68°25′ E) and results from a neural network model that reconstructs the fugacity of CO2 (fCO2) and fluxes at monthly scale. Anthropogenic CO2 (Cant) is estimated in the water column and is detected down to the bottom (1600 m) in 1985, resulting in an aragonite saturation horizon at 600 m that migrated up to 400 m in 2021 due to the accumulation of Cant. At the subsurface, the trend of Cant is estimated at +0.53±0.01 µmol kg−1 yr−1 with a detectable increase in the trend in recent years. At the surface during austral winter the oceanic fCO2 increased at a rate close to or slightly lower than in the atmosphere. To the contrary, in summer, we observed contrasting fCO2 and dissolved inorganic carbon (CT) trends depending on the decade and emphasizing the role of biological drivers on air–sea CO2 fluxes and pH inter-annual variability. The regional air–sea CO2 fluxes evolved from an annual source to the atmosphere of 0.8 molC m−2 yr−1 in 1985 to a sink of −0.5 molC m−2 yr−1 in 2020. Over 1985–2020, the annual pH trend in surface waters of -0.0165±0.0040 per decade was mainly controlled by the accumulation of anthropogenic CO2, but the summer pH trends were modulated by natural processes that reduced the acidification rate in the last decade. Using historical data from November 1962, we estimated the long-term trend for fCO2, CT, and pH, confirming that the progressive acidification was driven by the atmospheric CO2 increase. In 59 years this led to a diminution of 11 % for both aragonite and calcite saturation state. As atmospheric CO2 is expected to increase in the future, the pH and carbonate saturation state will decrease at a faster rate than observed in recent years. A projection of future CT concentrations for a high emission scenario (SSP5-8.5) indicates that the surface pH in 2100 would decrease to 7.32 in winter. This is up to −0.86 lower than pre-industrial pH and −0.71 lower than pH observed in 2020. The aragonite undersaturation in surface waters would be reached as soon as 2050 (scenario SSP5-8.5) and 20 years later for a stabilization scenario (SSP2-4.5) with potential impacts on phytoplankton species and higher trophic levels in the rich ecosystems of the Kerguelen Islands area.