Mesopelagic fish and squid occupy ocean depths extending below the photic zone and their verticalmigrations represent a massive pathway moving energy and carbon through the water column.Their spatio-temporal distribution is however, difficult to map across remote regions particularly thevast Southern Ocean. This represents a key gap in understanding biogeochemical processes, marineecosystem structure, and how changing ocean conditions will affect marine predators, which dependupon mesopelagic prey. We infer mesopelagic prey vertical distribution and relative abundance inthe Indian sector of the Southern Ocean (20° to 130°E) with a novel approach using predator-derivedindices. Fourteen years of southern elephant seal tracking and dive data, from the open ocean betweenthe Antarctic Polar Front and the southern Antarctic Circumpolar Current front, clearly show that thevertical distribution of mesopelagic prey is influenced by the physical hydrographic processes thatstructure their habitat. Mesopelagic prey have a more restricted vertical migration and higher relativeabundance closer to the surface where Circumpolar Deep Water rises to shallower depths. Combiningthese observations with a future projection of Southern Ocean conditions we show that changes in thecoupling of surface and deep waters will potentially redistribute mesopelagic prey. These changes aresmall overall, but show important spatial variability: prey will increase in relative abundance to the eastof the Kerguelen Plateau but decrease to the west. The consequences for deep-diving specialists such aselephant seals and whales over this time scale will likely be minor, but the changes in mesoscale verticalenergy flow have implications for predators that forage within the mesopelagic zone as well as thebroader pelagic ecosystem.