In the English Channel, the eastern Bay of Seine is exposed to numerous anthropogenic disturbances, in particular major changes in sediment dynamics, which are expected to greatly impact benthic communities. To assess the long-term effects of these stressors on the muddy fine sand benthic community, an original long-term monitoring program has been implemented since 1988. It is based on the sampling of a network of 60 stations during seven surveys over 28 years from 1988 to 2016. We investigate changes of species density, species composition and species diversity at different scales (α-diversity, β-diversity and γ-diversity). Contrary to results obtained in many coastal areas, our results showed a long-term persistence of the community in terms of species composition and structure although a general shift towards muddy sediment has resulted in increased colonisation by species associated with muddy habitats and a decrease in spatial beta diversity.