The dataset contains qualitative and quantitative data of mesozooplankton taxa collected in the framework of PN1920010 between 02 - 13 June 2020, from 8 stations (22 samples) located within a perimeter of 10 X 10 km2 in the northern part of the Romanian Black Sea (under the Danube influence) at 20 - 50 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). The samples were preserved in 10% formalin onboard and subsequently processed in the NIRD GeoEcoMar laboratory, according to Alexandrov et al,2014, by Mihaela Muresan. Identification was performed to the lowest taxonomic possible level. Individual and total abundances (ind.m-3) and biomasses (mg.m-3) were calculated according to Petipa et al., 1957, Alexandrov et al., 2014).