Here we show how routine acoustic data, primarily collected for stock assessment, allows for a 3D vision of the abiotic and biotic components of marine ecosystem and to study their interactions. Data, which can be obtained from any vessel geared with multi-frequency echosounders, provide relevant information to study the impact of physical processes on biogeochemical and ecological processes marine life and extracting valid information about the pelagic habitat and its spatial structure. All these data are to develop actual Ecosystem-based Fisheries Management in the current context of climate change. As an example we propose a synthesis of a scientific program developed in the Humboldt Current system off Peru which is the most productive in terms of fish and encompasses a shallow and intense oxygen minimum zone. © 2013 IEEE.