Earth’s climate is changing, and by the end of the 21st century in Europe, average temperatures are likely to have risen by at least 2 °C, and more likely 4 °C, with associated effects on patterns of precipitation and the frequency of extreme weather events. Attention among policy-makers is divided about how to minimise the change, how to mitigate its effects, how to maintain the natural resources on which societies depend and how to adapt human societies to the changes. Natural systems are still seen, through a long tradition of conservation management that is largely species-based, as amenable to adaptive management, and biodiversity, mostly perceived as the richness of plant and vertebrate communities, often forms a focus for planning. We argue that prediction of particular species changes will be possible only in a minority of cases but that prediction of trends in general structure and operation of four generic freshwater ecosystems (erosive rivers, depositional floodplain rivers, shallow lakes and deep lakes) in three broad zones of Europe (Mediterranean, Central and Arctic-Boreal) is practicable. Maintenance and rehabilitation of ecological structures and operations will inevitably and incidentally embrace restoration of appropriate levels of species biodiversity. Using expert judgement, based on an extensive literature, we have outlined, primarily for lay policy makers, the pristine features of these systems, their states under current human impacts, how these states are likely to alter with a warming of 2 °C to 4 °C and what might be done to mitigate this. We have avoided technical terms in the interests of communication, and although we have included full referencing as in academic papers, we have eliminated degrees of detail that could confuse broad policy-making.