The MGF Baltic Sea project investigates the impacts of mobile bottom-dwelling fisheries (MGF), which currently take place on a large scale in the Baltic Sea and include the Natura2000 protected areas within the German Exclusive Economic Zone (EEZ). The planned exclusion of fishing in parts of the protected areas offers a unique opportunity to study the impact of fishing on benthic biocoenoses and sediment functions and to analyse their regeneration potential. In the first phase of this project (MGF-Baltic Sea I), the current state of the benthic ecosystem was documented in the planned fishery exclusion areas as well as in comparable reference areas outside the protected areas (but immediately adjacent). An important result of this baseline survey was that the intensity of MGF, documented by fishing effort data and trawl marks in the sediment, was estimated to be comparably high in the reference and protected areas. Almost all ecosystem components, all organism groups from bacteria to fish, as well as the chemical-physical sediment parameters showed no significant differences between reference and protected areas. It can be assumed that the current MGF influence is responsible for the fact that biodiversity and sediment functions hardly differ between the protected and reference areas. This hypothesis will be tested in MGF Baltic II by continuing the investigations after fishery exclusion. Thus, the prerequisites are given to pursue the potential regeneration of biocoenoses after fishery exclusion in the protected areas with further comparative time series sampling of reference and protected areas. In addition, the baseline surveys for all protected areas are to be supplemented before fishing is excluded. With a focus on particularly meaningful parameters, non- or less-invasive methods (underwater video, eDNA, etc.) will also be tested, which can be used to document potential changes after fisheries have been excluded. In order to investigate short-term effects of MGF (e.g. sediment resuspension) and to test different fishing gear, a trawl experiment will also be conducted in an area close to the coast. The results will lead to a comprehensive assessment of the influence of MGF on benthic ecosystem functions as well as to the development of indicators for MGF-related disturbances. Furthermore, the results will lead to concrete recommendations for fisheries management and future monitoring strategies in protected areas.