Marine coastal ecosystems are among the most productive and diverse communities on Earth and are of global importance to climate, nutrient budgets, and primary productivity. Yet, these ecosystems, and in particular sedentary benthic (bottom-living) invertebrate communities at their base, are compromised by human-induced stresses, including overfishing, habitat destruction, and pollution. Emerging environmental legislation such as the Water Framework Directive (WFD) has the potential to significantly improve the ecological status of Europes 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 coastal systems, including flood defence, coastal development, dredging, aquaculture and fishing. There is a critical need for a set of biogeochemical measures to assist in the characterisation of ecological function, status and potential in coastal 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. As a complement to blind, synoptic sampling and laboratory studies, in situ studies provide rigorous scientific insight into the interactions between the biota (function and diversity) and their chemical and physical environment and the processes regulating this habitat within the context of dynamic processes that occur over many spatial and temporal scales. 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.