There have been considerable strides in Europe in support of holistic environmental management. Europe has begun to develop policy and fund research programmes in support of these broader approaches. Conceptual frameworks for basin-scale sediment management that address the complexities inherent in managing sediments at both a basin-wide and site-specific scale have been developed to integrate European regulatory and management approaches, and to define the interfaces between science, policy and economics. Emerging environmental legislation such as the Water Framework Directive (WFD) has the potential to significantly improve the ecological status of Europe's aquatic ecosystems, from rivers to the sea. However, depending upon how it is interpreted and implemented, it has the potential to impact many activities in aquatic systems, including flood defence, waterside development, dredging, aquaculture and fishing. There is a critical need for the development of scientifically rigorous biogeochemical measures to assist in the characterisation of ecological function, status and potential in benthic ecosystems. The FP6-funded Coastal Ocean Benthic Observatories (COBO, http://www.cobo.org.uk) program integrates in situ technologies to monitor benthic habitats, in order to understand how anthropogenic impacts affect benthic ecosystem functioning. COBO allows for interdisciplinary, in situ observation and experimentation in these complex, remote and poorly understood ecosystems, both providing fundamental understanding of the interactions between the biota and their environment and facilitating informed management of human impacts on coastal ecosystems. Conceptual frameworks and communication tools are being developed using visualisation software, advanced numerical tools and a DPSIR approach to link scientific results with policy, measures and approaches for coastal ecosystem management.