Fisheries acoustic instruments provide information on four major groups in aquatic ecosystems: fish with and without swim bladder (tertiary and quaternary consumers), fluidlike zooplankton (secondary consumers) and small gas bearing organisms such as larval fish and phytoplankton (predominantly primary producers). We entertain that this information is useable to describe the spatial structure of organism groups in pelagic ecosystems. The proposal we make is based on a multi-frequency indicator that synthesises in a single metric the shape of the acoustic frequency response of different organism groups, i.e. the dependence of received acoustic backscattered energy on emitting echosounder frequency. We demonstrate the development and interpretation of the multi-frequency indicator using simulated data. We then calculate the indicator for acoustic water-column survey data from the Bay of Biscay and use it to create reference maps for the spatial structure of the four scattering groups as well as their small scale spatial variability. These maps provide baselines for monitoring future changes in the structure of the pelagic ecosystem.