Mesopelagic fishes, a central component of marine trophic networks, play a fundamental role in marine ecosystems. However, as they live in highly inaccessible environments, little information is currently available on their distribution and abundance. The emergence of biologging technologies has made it possible to use deepdiving predators as bio-samplers of their environment in under-sampled regions. In this work, we deployed an innovative miniaturised sonar tag that combines active acoustics with high-resolution GPS, pressure, movement and light sensors on Southern elephant seals, a deep-diving predator feeding on mesopelagic prey. Seals were also equipped with Conductivity-Temperature-Depth tags. Salinity and temperature depth profiles were used to define oceanographic domains, allowing us to explore distribution and ecology of mesopelagic prey targeted by seals and the seals’ foraging behaviour. We highlighted strong vertical differences in prey characteristics and behaviour, with larger, more evasive and less bioluminescent prey in deeper waters. Moreover, prey encountered in warmer waters were found deeper, were more evasive and displayed a more marked diel vertical migration behaviour compared to prey encountered in colder waters, suggesting that prey accessibility and characteristics differ according to oceanographic domains. This study highlights the usefulness of the sonar-bioluminescence tag to infer mesopelagic prey distribution and habitat when deployed on deep-diving predators such as elephant seals.