Abstract During 2016–2017, the Indian Ocean experienced a pronounced increase in dissolved inorganic carbon (∼0.39 PgC/yr), approximately four times greater than the annual mean air–sea CO2 flux. Using a reconstructed data product and a state‐of‐the‐art ocean biogeochemical model, we attribute this anomaly to an enhanced Southern Ocean inflow and a weakened Indonesian Throughflow associated with an El Niño event accompanied by a positive Indian Ocean Dipole (IOD), and followed by a negative IOD during the El Niño‐to‐La Niña transition. The resulting carbon accumulation leads to a decline in aragonite saturation and a shoaling of the aragonite saturation horizon in the southeastern Indian Ocean. This subsurface acidification may pose risks to deep‐water calcifying organisms. Our findings demonstrate that ocean carbon storage and acidification are strongly modulated by circulation‐driven transport processes, highlighting the need for improved subsurface observations and model capabilities to better capture the interior carbon response to climate variability.

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