ABSTRACT: Commercial dredging for blue mussels (Mytilus edulis) and oysters (Ostrea edulis, Crassostrea gigas) constitute the main bivalve fisheries in Denmark. These activities predominantly take place in Limfjorden, a large microtidal sound, and in the Inner Danish waters. Both areas are shallow, estuarine, receive high nutrient inputs from agriculture, and are of nature conservation interest (Natura 2000 sites), thus presenting challenges for an ecosystem approach to fisheries management. Using high-resolution fisheries data (~10 m), we investigated the effects of bivalve dredging on benthic communities at both local (Natura 2000 site) and regional (fishery-wide) scales. Regionally, our results showed that dredging intensity correlated with shifts in species composition and reduced community biomass. We were, however, unable to detect an effect of dredging on community density, trait richness, and trait composition. These metrics were significantly related to other environmental drivers, such as sediment organic content (negative) and mussel bed biomass (positive). At the local scale, the observed relationships between dredging, biomass, and species composition varied significantly. This occurred as dredging impacts were greater in areas that contained suitable reference conditions and experienced relatively low levels of eutrophication and natural disturbance. By contrast, communities which experienced high nutrient loading, regular anoxic events, and high natural variability were relatively unaffected by dredging. Our results therefore highlight the importance of spatial scales in fishing impact estimations. Furthermore, we demonstrate how targeted sampling, high-resolution fisheries data, and suitable reference areas can be used to detect fishery effects in coastal areas that are highly stressed by eutrophication.