The dataset contains qualitative and quantitative data of mesozooplankton taxa collected in the framework of PN23300103, within 10 - 17 July 2023, from 14 stations (33 samples) located along 5 transects crossing the Romanian Black Sea shelf within 17 - 149 m bottom depths. The mesozooplankton samples were collected with a Juday net with 36 cm diameter opening and 150 µm mesh size towed from bottom to different discrete layers (thermocline, under thermocline, DCM) , onboard R/V Mare Nigrum. The samples were preserved in 10% formalin and subsequently processed in the NIRD GeoEcoMar laboratory, according to Alexandrov et al,2014. Taxonomic identification was performed to the lowest possible level. Individual and total abundances (ind.m-3) and wet biomasses (mg.m-3) estimation were calculated according to Petipa et al., 1957, Alexandrov et al., 2014.