Background The Baltic Sea is a unique and fragile marine ecosystem hosting many species and habitats of European and global interest, including the Steller's Eider (Polysticta stelleri) which has its own European Species Action Plan. It is believed that the by-catch of birds and seals in fishing nets is a problem in the Baltic Sea and assumed that habitats are damaged by construction works and the dumping of dredged material on the seabed. However, lack of data on the distribution and conservation status of habitats and species targeted by the Birds and Habitat Directives in the marine areas of Estonia, Latvia, and Lithuania remains a fundamental problem. Without this data or a clear understanding of environmental threats, the overall conservation objective cannot be achieved or measured. Objectives The project aimed to contribute to the protection and sustainable use of marine biodiversity in the costal and offshore waters of Estonia, Latvia and Lithuania - the Eastern Baltic Sea. A particular focus was to be given to the species and habitats mentioned in the relevant Annexes of European Directives. The detailed project objectives were to: 1. Obtain better information about species and habitats of European importance in the coastal waters of the Baltic States. 2. Assess and reduce the impact of fishery by-catch on target bird and mammal species, e.g. the priority species for LIFE funding Polysticta stelleri. 3. Assess and address other threats to marine Natura 2000 sites (e.g. caused by constructions/developments, disturbance of species by economic or recreational activities, pollution). 4. Complete the establishment of Natura 2000 in the marine territories of Estonia, Latvia and Lithuania (site selection, designation, protection rules and management plans). 5. Increase public and stakeholder awareness on Natura 2000, marine protected areas and biodiversity in general in Estonia, Latvia, Lithuania and Russia. Trans-boundary networking and capacity building with key stakeholders from north-west Russia was also foreseen due to the close ecological connectivity of the Baltic Sea ecosystem and serious (potential) threats originating from the adjacent non-EU territories. Results The project successfully provided a scientifically sound basis for designation of MPAs and mitigation measures for targeted marine habitats and species. Following appropriate training and study visits, the team studied benthic (seabed) habitats in 13 areas totalling 6 000 km2. Ecologically important reef and sandbank habitats were found to be rare. Fish species were monitored using nets with meshes of different sizes and food analysis of larger fish. An inventory of waterbirds from land, ships and planes identified breeding sites and spotted endangered birds. Acoustic monitoring devices, tags and an aerial census discovered that the harbour porpoise (Phocoena phocoena) was not present, but found growing populations of grey seal (Halichoerus grypus) and struggling populations of ringed seal(Pusa hispida). Data was gathered from co-operating fishermen on species caught in their gear, complemented with information from independent project fishing activities. Hydro-dynamical modelling assessed the impact to marine habitats from the dumping of dredged material and a literature review assessed impact from various economic activities. Finally, pollution levels from shipping, oil and other industries were measured by sampling molluscs and sediment. The main threats to the ringed seal were the warming climate and human disturbance to breeding and resting sites. Fishing by-catch was a cause of mortality for seals, birds and non-commercial fish but it was generally not a major threat to populations. Nor was dumping of dredged material a major issue within protected areas. Far more important factors were eutrophication and pollution of water. The project proposed seven new marine protected areas in Latvia, one in Lithuania and the modification of existing ones in Lithuania and Estonia. The team conceived management plans for six areas, describing the sites and proposing modest restrictions to some military and leisure activities. Larger mesh sizes and some calendar restrictions were proposed for Lithuanian fishermen. Use of long lines and herring-trap nets to reduce bird catch in cod and herring fishing were demonstrated effectively in Lithuania. In Estonia, seal-safe fyke nets were successfully tested for protecting seals and reducing damage to nets, earning the support of local fishermen and the European Fisheries Fund. The project engaged key stakeholders - including Russian partners - in activities and events to raise their awareness of Natura 2000 in marine environments. Supporting materials included a film, a book, flyers, a website and information boards. Further information on the project can be found in the project's layman report and After-LIFE Conservation Plan (see "Read more" section).