By relating observed changes to the pressures suffered, the Marine Strategy Framework Directive intends to better control the factors of environmental degradation and to manage their consequences in European waters. Several descriptors are defined within the framework of the MFSD and in particular descriptor 1 relating to the biological diversity of the seabed and descriptor 6 relating to the seabed integrity (i.e. the quality of their structures and functions). For each descriptor, indicators and threshold values must be defined and a novel conceptual approach to define and detect seabed integrity thresholds is proposed here. Bottom trawling being the main source of shelf continental disturbance, it is important to evaluate its impact on benthic habitat. The goal of this study is to propose a methodology to determine “Good Ecological Status” threshold values for each habitat type present in three contrasted MFSD sub-region (North Sea, English Channel and Mediterranean Sea). Trawling impacts are dependent of the spatial and temporal distribution of the fishing effort, fishing gears, intensity of natural disturbances and habitat types. Benthic community structures present in these areas were studied using by-catch non-commercial benthic invertebrates data collected during French scientific bottom trawl surveys. Swept area ratios derived from VMS data were used to quantify the intensity of fishery induced abrasion on the seabed. A modeling approach was used to determine abrasion threshold values on each EUNIS level 4 habitat. The values, beyond which trawling has an adverse effect on benthic communities, have been determined for each habitat. This made it possible to assess and map the ecological status of each of the habitats and to determine the percentage of each habitat impacted by trawling. The method proposed here to evaluate the impact of trawling on benthic communities highlighted that the vast majority of the investigated sub-regions were adversely impacted or lost as a result of seabed impacting trawling.