<em>Abstract.</em>—The St. Lawrence estuarine transition zone (ETZ) harbors the only known concentrations of age-0 and early juveniles of the St. Lawrence Atlantic sturgeon and lake sturgeon populations. Past dredging and disposal operations conducted in the ETZ to deepen the navigation channel resulted in the creation of an extensive sand dune biotope near the juvenile sturgeon concentration areas. In order to characterize the dune biotope within a diversified set of biotopes in the ETZ, nine areas were selected for study, including two areas to cover the sand dune complex. The study objectives were (1) to identify the benthos assemblages of the ETZ and the main physical factors controlling them, (2) to measure the sampling areas’ biological characteristics and feeding potential for sturgeon, and (3) to compare the dune areas’ feeding potential with selected control areas. In 1999–2001, grab sampling was conducted at 141 stations to determine macrobenthos composition and sediment parameters. Depth, slope, and slope orientation were measured from multibeam sonar echosoundings. Salinity, current velocity, and tidal amplitude were provided by a hydrodynamic model of the ETZ. Benthos assemblages were determined using cluster analysis on taxon biomass. Four major assemblages were identified, all having Tubificidae as the dominant or subdominant taxon: zebra mussel <em>Dreissena polymorpha</em>, <em>Gammarus tigrinus</em>, Tubificidae, and <em>Capitella</em> sp. assemblages. A succession of the major assemblages was observed from the freshwater front to the upper mesohaline waters. Three minor assemblages, the Chironomidae, Physidae, and Cumacea, were concentrated in the upper oligohaline zone. Taxonomic richness was highest in areas with the lowest maximum salinity (0.0–0.5), and diversity was highest in areas with intermediate maximum salinities (0.5–2.0). The largest biomass values were found in areas with maximum salinities less than 0.5, in the zebra mussel assemblage. Controls and dune areas had similar macrobenthos richness and diversity, but dune areas had significantly lower densities and biomasses. Feeding potential for a given sturgeon life stage was measured as the sum of taxa biomasses standardized using the prey proportions in that life stage’s feeding regime. For age-0 Atlantic sturgeon and for all lake sturgeon life stages, all of which feed mostly on gammarids, the feeding potential of control and dune areas were not significantly different. For juvenile and subadult Atlantic sturgeon, which feed mostly on tubificids, the dune areas had a significantly lower feeding potential than the control areas. The lower feeding potential of the sand dune areas created by dredged sediment deposition is considered an important issue for the management of the St. Lawrence Atlantic sturgeon population.