Current research revealed distinct changes in ecosystem functions, and thus in ecosystem stability and resilience, caused by changes in community structure and diversity loss. Even if benthic species play an important role in benthic-pelagic coupling e.g. through the remineralization of deposited organic material, the long-term variability of traits and functions is largely unknown. By using abundance and bioturbation potential of macrofauna samples, taken along a transect from the German Bight towards the Dogger Bank annually in May in 1990 and from 1995 to 2017, we analysed the taxonomic and trait-based macrofauna long-term community variability and diversity. Taxonomic and trait-based diversity remained stable over time, while three different regimes were found, characterised by changes in taxonomic and trait-based community structure. Min/max autocorrelation factor analysis revealed climatic variables, nitrite, and epibenthic abundance as most important environmental drivers for taxonomic and trait-based changes.