The dataset comprises data on the substrate type, temperature, salinity, oxygen saturation, and macrozoobenthos from samples colleceted at several stations in the Black Sea in 2003–2011. The sediment samples were taken with a Van-Veen grab. The sediment was preserved in buffered formalin 4% , then sieved through a 1 mm, 0.5 mm and 0.10 mm mesh sieve and subsequently stored in 70% ethanol. The database comprises taxonomic and quantitative data (density and wet weight biomass per square meter).