The dataset contains macrozoobenthos data collected during the MN248 Cruise, from 3 stations located in the Romanian Black Sea area, in 1-10 September 2023, in the framework H2020 DOORS Project. The main goal of the cruise was to assess the sediment nutrients cycling capacity and the influence of faunal activity on benthic turnover rates of nutrient and oxygen through ex-situ sediment core incubation. The data acquisitions was focused on three main benthic habitats, as follows: coarse and mixed biogenic type of substrata suitable for thriving of mussel’s biogenic reefs and mud sediments under river plume influence. From each station, three replicates were collected with the Multicorer (the sampling size - 0.079 m2) and three with Van-Veen grab (the grasping area - 0.125 m2). The sediment was preserved in buffered formalin 4% , then sieved through a 1 mm and 0.5 mm mesh sieve and subsequently stored in 70% ethanol. The database comprises taxonomic and quantitative data (density and wet weight biomass per square meter) for 69 macrozoobenthic species and 2 supraspecific groups.