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1. We review recent advances in systematic conservation planning in fresh waters. Most modern systematic planning approaches are based on the CARE principles: comprehensiveness, adequacy, representativeness and efficiency. Efficiency is usually provided by a complementarity‐based strategy, aiming to select new conservation areas in the light of previously protected features. These strategies have to be modified to account for the connected nature of rivers.

2. Choice of surrogates for conservation features depends on the scale of the assessment, as well as the available expertise and resources. Ideally, real information about taxa or processes – extrapolated by models – ensures that target features are protected. Where this is not feasible, it is critical that the choice of environmental surrogates is informed by target biota or processes.

3. Setting adequacy targets – the most challenging aspect in planning …