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Abstract The AQUACROSS project was an unprecedented effort to unify policy concepts, knowledge, and management of freshwater, coastal, and marine ecosystems to support the cost-effective achievement of the targets set by the EU Biodiversity Strategy to 2020. AQUACROSS aimed to support EU efforts to enhance the resilience and stop the loss of biodiversity of aquatic ecosystems as well as to ensure the ongoing and future provision of aquatic ecosystem services. The project focused on advancing the knowledge base and application of Ecosystem-Based Management. Through elaboration of eight diverse case studies in freshwater and marine and estuarine aquatic ecosystem across Europe covering a range of environmental management problems including, eutrophication, sustainable fisheries as well as invasive alien species AQUACROSS demonstrated the application of a common framework to establish cost-effective measures and integrated Ecosystem-Based Management practices. AQUACROSS analysed the EU policy framework (i.e. goals, concepts, time frames) for aquatic ecosystems and built on knowledge stemming from different sources (i.e. WISE, BISE, Member State reporting within different policy processes, modelling) to develop innovative management tools, concepts, and business models (i.e. indicators, maps, ecosystem assessments, participatory approaches, mechanisms for promoting the delivery of ecosystem services) for aquatic ecosystems at various scales of space and time and relevant to different ecosystem types. Graphical abstract Unlabelled Image Highlights • We describe the aims and approaches of the EU-funded Horizon 2020 project AQUACROSS, its conceptual framework and case studies. • AQUACROSS aims to demonstrate practical applications of the Ecosystem Based Management concept. • AQUACROSS considers the management of aquatic ecosystems as a continuum, from freshwater to marine through coastal areas. • The project addresses multiple interactions between socio-economic and ecological systems in aquatic ecosystems • It includes eight case studies across Europe, all with different scales (temporal, spatial, at different levels of ecosystem organization). [ABSTRACT FROM AUTHOR]