Characterised by long term cooling and abrupt ice sheet expansion on Antarctica ~14 Ma ago, the mid Miocene marked the beginning of the modern ice-house world, yet there is still little consensus on its causes, in part because carbon cycle dynamics are not well constrained. In particular, changes in carbonate ion concentration ([CO32−]) in the ocean, the largest carbon reservoir of the ocean-land-atmosphere system, are poorly resolved. We use benthic foraminiferal B/Ca ratios to reconstruct relative changes in [CO32−] from the South Atlantic, East Pacific, and Southern Oceans. Our results suggest an increase of perhaps ~40 μmol/kg may have occurred between ~15 and 14 Ma in intermediate to deep waters in each basin. This long-term increase suggests elevated alkalinity input, perhaps from the Himalaya, rather than other shorter-term mechanisms such as ocean circulation or ecological changes, and may account for some of the proposed atmospheric CO2 decline before ~14 Ma.