The dataset contains qualitative and quantitative data of mesozooplankton taxa collected in 20 - 30 July 2024, in the framework of PN23300103, from 11 stations (22 samples) located along 5 transects crossing the Romanian Black Sea shelf within 16 - 1115 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 surface, 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 conducted according to Petipa et al., 1957, Alexandrov et al., 2014).