Given the increasing international pressure towards the reduction of the impacts of fishing on the ecosystem, Canada must develop research programs to evaluate the influence of fisheries and design innovative fishing gears preserving the seabed. Epibenthic macrofauna was monitored at 758 stations in the lower estuary and northern Gulf of St. Lawrence each summer between 2006 and 2009. This first large-scale characterization of benthic macrofauna using multivariate, geostatistical, and mapping approach aims at 1) describing spatial distribution of benthic communities and their species composition, 2) analyzing links between communities and environmental variables (such as depth, temperature, oxygen saturation, bottom current, sediment), and 3) using a predictive distribution model to create a full-coverage habitat suitability map. Results from the prediction model allow the identification of zones of greater and lesser suitability for specific species and community types. The resulting maps can be used to evaluate the impacts of fisheries on the seabed habitat structure, and therefore used for management of the marine space and conservation of both fishing stocks and vulnerable non-fished species.