Benthic habitat mapping is an important first step towards ecosystem-based management. In a top-down approach, benthic mapping of a semi-enclosed bay in south-eastern Brazil was performed using a combined approach of acoustic RoxAnn survey and benthic samples. An inventory of the benthic macrofauna as well as unsupervised classifications of the acoustic data provided information about sediment patterns and potential areas of ecological importance, and a new zoning scheme is suggested based on the macrofauna analysis. The RoxAnn survey proved suitable to determine sediment characteristics, however, species-environment relationships cannot be revealed by acoustic techniques only. Based on the data presented here, acoustic surveys could become an important tool in future monitoring programmes following the bottom-up approach of seabed classification protocols for an ecosystem-based management to improve existing coastal ecosystem management strategies in Brazil.