The North-Western Black Sea shelf is extremely vulnerable to disturbances of its habitats and ecosystems. In the past 10 years, this area has become targeted by beam trawl fisheries for the invasive gastropod Rapana venosa (Valenciennes, 1846), with a potentially destructive impact on the area’s soft bottoms. Not many studies have been performed in the region, and most investigations have focused on gear selectivity and by-catch rates. In this context, our novel research aimed, on the one hand, to assess and quantify the actual impact of beam trawling and, on the other hand, to propose effective spatial/temporal management measures for a sustainable zonation of the North-Western Black Sea shelf (marine zone of the Danube Delta Biosphere Reserve). The methodology used integrated beam trawl catch dynamics information, VMS data, geophysical investigations, and macrozoobenthos sampling. Our findings show that beam trawling activities can cause changes in the benthic habitat structure (lower number of taxa, lower values of ecological indicators, and an overall non-GES status). Further in-depth investigations are needed to underpin the ecosystem-based management of this marine protected area (MPA), aiming to allow the recovery of the affected benthic habitats, by alternating defined areas undergoing fishing with biological recovery polygons.