Spatial distribution patterns of benthic littoral fauna were studied over a 12 yr period in a large subarctic ecosystem, the Estuary and northwestern Gulf of St. Lawrence. Binary presence-absence data obtained from suspended collectors (navigation buoys) moored yearly, from May through November, were used to examine ecological affinities and spatial heterogeneity in species distribution. Analyses of species co-occurrence followed by arithmetic average clustering, conducted at large (whole system, Gulf, Estuary) and intermediate (North Shore plus Lower North Shore) spatial scales, revealed a recurrent species association (composed of 12 species including Obelia longissima, Mytilus edulis, Balanus crenatus, Hiatella arctica, and Semibalanus balanoides) characterizing the entire Estuary-Gulf area. Frequency analyses carried out along 3 potential pathways of larval dispersal made it possible to identify major spatial discontinuities in species distribution as well as the community members contributing most to them, The outstanding changes in composition and distribution of benthic species throughout the study area were highly coincident with well-defined physiographical (e.g. presence of straits, islands, contour of shoreline) and hydrographical (e.g. zones of freshwater inputs, upwellings, frontal zones) features of the system, particularly along the estuarine gradient.