Abstract Distribution patterns and species composition of macrozoobenthos were studied in the Dutch coastal zone in front of the Port of Rotterdam. Relationships between macrozoobenthic assemblages and environmental variables were determined using non-metric dimensional scaling (nMDS) based on 470 boxcore, bottom sledge, and sediment samples collected in spring 2006 and 2008 in a 2500-km2 research area. We investigated two types of benthic assemblages, infaunal assemblages sampled with a boxcorer and epifaunal assemblages sampled with a bottom sledge. Five main in- and epifaunal assemblages were distinguished using clustering techniques and nMDS ordinations. Macrozoobenthic species composition correlated with combinations of measured sediment variables and modelled hydrodynamic variables. Macrozoobenthic species richness and biomass were highest at 20 m deep areas with a grain size of 200 µm, elevated mud and sediment organic matter, and low mean bed shear stress. Considerable interannual differences in macrozoobenthic assemblage distribution were observed which resulted from more Echinoids, Phoronids, and jackknife clams. A distinct, highly productive and species-rich macrozoobenthic white furrow shell Abra alba assemblage coincided in a 8-m deepened shipping lane and near a disposal site for dredged fine sediment. This may be an indication that the benthic system can be changed by these human activities. Modelled bed shear stress is an important variable in addition to sediment variables in explaining distribution patterns in macrozoobenthos.