Background Marine biodiversity indicators are tools that enable changes in biological components of marine ecosystems to be identified and followed. They also enable those changes to be linked with pressures, and help in the assessment of the effectiveness of measures taken to reduce those pressures on different geographical scales, thereby providing a basis for informed decision making and adaptive management. However, a common understanding of indicators for assessing the biodiversity status of the Baltic Sea, according to existing European legislation and international agreements, does not yet exist. Quality objectives, as well as aspirational indicators, have been determined in the HELCOM Baltic Sea Action Plan and EU legislation, but precise indicators and their methodology still need to be developed. Currently, several projects and working groups are dealing with this issue, including the MARMONI project which reviewed the existing sets of marine biodiversity indicators and elaborated a new set based on targets for good environmental status according to the Marine Strategy Framework Directive. Nevertheless, the main threats to the habitats and associated species to be monitored are the presence of non-native species, eutrophication caused by diffuse pollution, and oil spills from shipping. Objectives The MARMONI project aimed to develop concepts for assessing the conservation status of marine biodiversity and to quantify the impacts of various human activities. Focusing on the Baltic Sea territorial waters and the EEZ (Exclusive Economic Zone) of Estonia, Latvia, Finland and Sweden, the aim was to apply a regional approach for future marine biodiversity monitoring and international co-operation when assessing marine biodiversity in the Baltic Sea. Specific project objectives included the development of new ecosystem-based monitoring and assessment approaches, using marine biodiversity indicators, to assess the conservation status of species and habitats and impacts of human activities; to test these integrated assessment techniques and biodiversity indicators, as well as special techniques and equipment for monitoring, in pilot demonstration cases; and to develop criteria and demonstrate how nature conservation and land-use in marine areas can be balanced in a sensitive way. Results The MARMONI project developed and tested 49 true marine biodiversity indicators for four species groups: 16 for bird, 8 for fish, 15 for benthic, and 10 for pelagic species. Altogether, 17 new or innovative monitoring methods were tested in four study areas in the Baltic Sea. The results were collated in the key project publication entitled ‘The MARMONI approach to marine biodiversity indicators’. An online database of all the MARMONI biodiversity indicators was developed and made available (http://www.sea.ee/marmoni/marmoni_pulk/start_indicator_database.html). Biodiversity assessment was carried out for target habitats and species in each of the four project pilot areas: Irbe Strait and the Gulf of Riga (Latvia and Estonia), Hanö Bight (Sweden), Coastal Area of SW Finland, and Gulf of Finland (Estonia and Finland). An assessment of Favourable Conservation Status (FCS) of species and habitats in line with the Habitats Directive was performed in these pilot areas. The project demonstrated marine spatial management in Sweden, based on maps of the same ecosystem components as the biodiversity indicators, using the same survey methods. Thus, biodiversity assessment has been linked to the planning processes. A common marine biodiversity monitoring assessment scheme for the Baltic Sea region was prepared. The results of this assessment were presented in the report ‘Socio-economic assessment of indicator-based marine biodiversity monitoring programmes and methods’. The project assessed the cost-effectiveness and cost-efficiency of the indicator-based monitoring programmes and methods. The indicators have been applied according to the Good Environmental Status (GES) of the Marine Strategy Framework Directive (MSFD). MARMONI produced recommendations for national marine monitoring programmes, and for the national marine protection policies of Latvia, Estonia, Finland and Sweden, with the aim of facilitating uptake of the project’s results in the policy-making process for protection marine biodiversity. Three essential components were addressed: existing legal frameworks, monitoring, and environmental impact assessment (EIA) procedures. A set of indicators and monitoring methods proposed by MARMONI are already included in national monitoring programmes. They have also served to help develop HELCOM indicators, within projects aiming to harmonise marine monitoring at the Baltic Sea Region level. A MSFD-compliant, indicator-based marine biodiversity assessment tool was developed using experiences from previously available tools used in HELCOM, and recent scientific findings. After testing, further improvements were made to the tool and additional functionality was added (e.g. GIS module). The final MARMONI Biodiversity Assessment Tool, incorporating the project’s biodiversity indicators, was made available online (http://www.sea.ee/marmoni/index.php). Different innovative approaches were applied during the project (e.g. aggregation principle, scoring system of the assessment result, use of different types of indicators), and two new innovative bird monitoring methods (aerial imaging using high-resolution RGB and thermal image sensors) were also tested. Although monitoring activities were performed within the four pilot areas, a regional integrated approach was possible and several methods (e.g. drop-video, diving, benthic grab sampling, aerial bird surveys, satellite and air-borne remote sensing, gill-net and beach seine) were performed in several areas. The project’s monitoring and modelling techniques can be easily replicated and are applicable for use in the entire Baltic Sea area. The project organised a series of national meetings with stakeholders in Latvia, Estonia, Sweden and Finland. A total of 33 training events were also carried out in these countries. MARMONI’s results have been promoted at various international conferences and seminars. The project produced a series of posters and brochures on marine nature for the layperson, which were made available in strategic public places, such as on Tallink ferries, in museums and in information centres. The project’s results are helping with the implementation of the EU MSFD, and the Habitats and Birds Directives, in the project countries; and at the Regional Sea Conventions (RSC) and Baltic Marine Environment Protection Commission (HELCOM) levels, to improve the status of marine biodiversity in the Baltic Sea. Further information on the project can be found in the project's layman report and After-LIFE Conservation Plan (see "Read more" section).