Despite expanding in-situ observations of marine ecosystems by new-generation sensors, information about intermediate trophic levels remains sparse. Indeed, mid-trophic levels, while encompassing a broad range of zooplankton and micronekton organisms that represent a key component of marine ecosystems and sustain large and diverse communities of marine predators, are challenging to sample and identify. In this study, we examined whether an animal-borne miniature active echosounder can provide information on the distribution and movements of mid-trophic level organisms. If so, such a sonar tag, harnessing the persistent diving behaviour of far-ranging marine mammals, could greatly increase the density of data on this under-studied biome. High-frequency (1.5 MHz) sonar tags were deployed simultaneously with oceanographic tags on two southern elephant seals (Mirounga leonina), at the Kerguelen Islands and Valdés Peninsula (Argentina), and recorded acoustic backscatter while the seals foraged respectively in the Indian and the Atlantic sectors of the Southern Ocean. The backscatter varied widely over time and space, and the seals attempted to capture only a small fraction of the insonified targets. Diel vertical migration patterns were clearly identifiable in the data, reinforcing our confidence in the ability of the sonar tags to detect living mid-trophic organisms along with possibly sinking biological detritus. Moreover, CTD tags attached to the same animals indicated how the abundance, size distribution, and diel migration behaviour of acoustic targets varied with water bodies. These preliminary results demonstrate the potential for animal-borne sonars to provide detailed in-situ information. Further validation effort will make it a valuable tool to refine the estimation of carbon export fluxes as well as for assessing the variation of mid-trophic level biomass according to oceanographic domains and seasons.