We argue for improved conservation of freshwater ecosystems at catchment or eco-regional scales by explicit assignment of values to all river sections and wetlands, recognising current disturbance, and aiming for ‘no further harm’ to the commons. The need is indicated by the global deterioration of biodiversity and ecosystem services of rivers and wetlands, increasing demands on water and land resources, and climate change. Regional pressures include multiple jurisdictions, competing demands, piecemeal management, pollution and habitat impacts. Effective resource and conservation management needs to integrate multiple uses via governance of activities of stakeholders, recognising hydrogeomorphic, water quality and ecological properties of ecosystems. Complete ecological protection is impractical amidst water-resource and land-use development, but we suggest that all river reaches and wetlands be given a conservation rating based on habitat, biodiversity and connectivity values. We present a straightforward approach to spatial conservation rating of freshwaters, using hydrogeomorphic typology and assignment of conservation values on the basis of available information and expert elicitation. We illustrate the approach by using the large Burdekin River catchment in north-eastern Australia. This approach is complementary to more spatially focused conservation prioritisation and could greatly improve management for sustainability, reduce further decline in conservation values, and facilitate rehabilitation.