The European Union Water Framework Directive (WFD) represents a new approach to the management of water across Europe. As part of the implementation of the WFD, integrated, catchment-scale plans for the protection and restoration of aquatic ecosystems must be developed. These plans need to be supported by new science, focused on understanding the general modes of behaviour of complex aquatic ecosystems, and the fundamental principles that govern this behaviour. This requires the collaborative production of new scientific knowledge, drawing on expertise from multiple academic disciplines, and refocusing on larger spatial and longer temporal scales. To mobilise existing scientific knowledge, and to produce new knowledge that is effectively adopted in policy and practice, scientists and managers must also develop collaborative partnerships involving the co-production and bidirectional exchange of knowledge. However, many personal and institutional barriers currently limit the development of such partnerships. Particular issues surround individual willingness to step outside disciplinary comfort zones, and the role of professional norms, rewards and value systems. The lack of training and support for individual knowledge-brokers, who work to develop these partnerships at the interface between science and management, is also a limiting factor. Even with such collaborative partnerships in place between scientists, and between scientists and managers, scientific knowledge will only ever be one contributor to the decision-making processes occurring within the WFD. Scientific knowledge will compete alongside issues of personal and institutional values, of moral judgements, of equity and of social justice in the consensus-building processes occurring within decision-making fora. The potential for, and the limits of, scientific knowledge to support the implementation of the WFD should be clearly recognised.