The bioacoustics of upper waters of the Black Sea, the Sea of Marmara, and the Mediterranean Sea were studied in October 1999 with an echosounder with 120 and 200 kHz dual-beam transducers. Net tows were taken to ground-truth the acoustic volume backscattering. A forward solution was applied to determine significant scatterers of the three seas with regard to detection limits of the frequencies and background noise measured in each sea. The noise was 4 dB higher in the Sea of Marmara than in the other two seas. 200 kHz data showed significant correlation between measured and calculated volume backscattering strength, and density (biomass and abundance) of the taxa. Large-sized copepods and chaetognaths in the Black Sea, Aurelia, Beroe, chaetognaths and large-sized and abundant appendicularians in the Sea of Marmara, and fish larvae in the Mediterranean Sea contributed most to the volume backscattering.