Continental shelves encompass gently sloped seascapes that are highly productive and intensively exploited for natural resources. Islands, reefs and other emergent or quasi-emergent features punctuate these shallow (<100 m) seascapes and are well known drivers of increased biomass and biodiversity, as well as predictors of fishing and other human uses. On the other hand, relict mesoscale geomorphological features that do not represent navigation hazards, such as incised valleys (IVs), remain poorly charted. Consequently, their role in biophysical processes remains poorly assessed and sampled. Incised valleys are common within rhodolith beds (RBs), the most extensive benthic habitat along the tropical and subtropical portions of the mid and outer Brazilian shelf. Here, we report on a multi-proxy assessment carried out in a tropical-subtropical transition region (~20°S) off Eastern Brazil, contrasting physicochemical and biological variables in IVs and adjacent RBs. Valleys interfere in near bottom circulation and function as conduits for water and propagules from the slope up to the mid shelf. In addition, they provide a stable and structurally complex habitat for black corals and gorgonians that usually occur in deeper water, contrasting sharply with the algae-dominated RB. Fish richness, abundance and biomass were also higher in the IVs, with small planktivores and large-bodied, commercially important species (e.g. groupers, snappers and grunts) presenting smaller abundances or being absent from RBs. Overall, IVs are unique and vulnerable habitats that sustain diverse assemblages and important ecosystem processes. As new IVs are detected by remote sensing or bathymetric surveys, they can be incorporated into regional marine management plans as conservation targets and priority sites for detailed in situ surveys.