This second special issue of the Journal of Sea Research on development and applications of Dynamic Energy Budget (DEB) theory concludes the European Research Project AquaDEB (2007–2011). In this introductory paper we summarise the progress made during the running time of this 5 years’ project, present context for the papers in this volume and discuss future directions. The main scientific objectives in AquaDEB were (i) to study and compare the sensitivity of aquatic species (mainly molluscs and fish) to environmental variability within the context of DEB theory for metabolic organisation, and (ii) to evaluate the inter-relationships between different biological levels (individual, population, ecosystem) and temporal scales (life cycle, population dynamics, evolution). AquaDEB phase I focussed on quantifying bio-energetic processes of various aquatic species (e.g. molluscs, fish, crustaceans, algae) and phase II on: (i) comparing of energetic and physiological strategies among species through the DEB parameter values and identifying the factors responsible for any differences in bioenergetics and physiology; (ii) considering different scenarios of environmental disruption (excess of nutrients, diffuse or massive pollution, exploitation by man, climate change) to forecast effects on growth, reproduction and survival of key species; (iii) scaling up the models for a few species from the individual level up to the level of evolutionary processes. Apart from the three special issues in the Journal of Sea Research –including the DEBIB collaboration (see vol. 65 issue 2), a theme issue on DEB theory appeared in the Philosophical Transactions of the Royal Society B (vol 365, 2010); a large number of publications were produced; the third edition of the DEB book appeared (2010); open-source software was substantially expanded (over 1000 functions); a large open-source systematic collection ecophysiological data and DEB parameters has been set up; and a series of DEB tele-courses and symposia have been further developed and expanded, bringing together people from a wide variety of backgrounds (experimental and theoretical biologists, mathematicians, engineers, physicists, chemists, environmental sciences, computer scientists) and training levels in DEB theory. Some 15 PhD students graduated during the running time of AquaDEB with a strong DEB component in their projects and over 15 will complete their thesis within a few years. Five post-doctoral projects were also part of the training network. Several universities (Brest, Marseille, Lisbon, Bergen) included DEB courses in their standard curriculum for biology students.