Abstract The Water Framework Directive (WFD) embodies concepts of “ecological health”. This essay extends this metaphor, looking at the ways in which ecologists should diagnose and treat “sick” ecosystems. Recent practice in the UK has been to develop multifunctional ecologists to act as ecological equivalents of “family doctors”. This requires methods that can be used without high levels of specialisation and, in turn, allows individuals to gain deep knowledge of particular geographic areas. This system is under threat both from new scientific developments and from management innovations designed to reduce costs. The next stages of WFD implementation, however, will see a shift towards locally based problem-solving, where inherent uncertainties will require the exercise of professional judgement above and beyond evidence-based science. We need to encourage “breadth” as well as “depth” in ecological assessment methods and a three-tiered framework for this is described.