Relationships between benthic macrofauna and natural abiotic factors were studied along the coastal fringe of South Brittany, situated north of the Gulf of Biscay on the French Atlantic continental shelf. Within the framework of the REBENT network, sediment characteristics, depth, and macrofaunal abundance were determined for 95 stations spread over five subtidal sectors, using a combination of seabed acoustic remote sensing systems and grab sampling. The physico-chemical properties of the water column and the hydrodynamic conditions were generated by validated three-dimensional environmental models which take into account variations over shorter temporal scales. Multivariate analyses ranked 16 natural abiotic variables according to the significance of their influence on the macrofauna. Together these variables explained 51% of spatial variation in the macrofauna, with morpho-sedimentological and hydrological factors contributing 22% and 26%, respectively. The outputs from validated three-dimensional environmental models appear to be useful interpretational tools for benthic ecology studies, especially in estuarine and coastal ecosystems with high environmental variability due to regular freshwater inputs. Ten major species assemblages were identified using biological and physical characteristics. The results provide important baseline knowledge for future ecosystem and resource management.