The extended multiple linear regression (eMLR) technique is used to determine changes in anthropogenic carbon in the intermediate layers of the Eurasian Basin based on occupations from four cruises between 1996 and 2015. The results show a significant increase in basin‐wide anthropogenic carbon storage in the Nansen Basin (0.44‐0.73 ± 0.14 mol C m−2 yr−1) and the Amundsen Basin (0.63‐1.04 ± 0.09 mol C m−2 yr−1). Over the last two decades, inferred changes in ocean acidification (0.020‐0.055 pH units) and calcium carbonate desaturation (0.05‐0.18 units) are pronounced and rapid. These results, together with results from carbonate‐dynamic box model simulations and 129I tracer distribution simulations, suggest that the accumulation of anthropogenic carbon in the intermediate layers of the Eurasian Basin are consistent with increasing concentrations of anthropogenic carbon in source waters of Atlantic origin entering the Arctic Ocean followed by interior transport. The dissimilar distributions of anthropogenic carbon in the interior Nansen and Amundsen Basins are likely due to differences in the lateral ventilation of the intermediate layers by the return flows and ramifications of the boundary current along the topographic boundaries in the Eurasian Basin.