Echo-sounders and Vessel-Mounted Acoustic Doppler Current Profilers (VM-ADCP) are widely operating onboard research vessels with the aim of providing real-time backscatter and ocean current profiles along the route, while the vessel is moving. Backscatter data are exploited to infer important information about zooplankton presence and distribution. Nevertheless, as these organisms daily vertically migrate even below the depth of the instrument range, the combination of space and time variability make their mapping from a moving vessel quite complex. The objective of this work is to describe a GIS application developed for the management and analysis of these data. The GIS capability as a tool to facilitate zooplankton investigations is assessed by means of a test-case in the area of the Ligurian Sea (Western Mediterranean) by using VM-ADCP backscatter data made available during oceanographic campaigns. The system, which includes a high-resolution bathymetry, environmental parameters, ephemeris, allows to select and visualize data sorted according to all the possible layer combinations. Moreover, different backscatter profiles, characterizing the identified migration phases can be enlightened by means of false color scale representation.