The dataset contains qualitative and quantitative data of mesozooplankton taxa collected in 29 July - 02 August 2022 in the framework of PN19200102, from 12 stations located along 6 transects crossing the Romanian Black Sea shelf within 15.5 - 65 m bottom depths. The mesozooplankton samples were collected using a Juday net with 36 cm diameter opening and 150 µm mesh size towed from bottom to certain depth intervals (surface, thermocline, under thermocline) or integrally 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) were calculated according to Petipa et al., 1957, Alexandrov et al., 2014.