1. Although the freshwater environments of New Zealand once comprised an extensive interconnected network of rivers, lakes, and wetlands, their extent, condition, and connectivity have been reduced since human settlement, with consequent impacts on ecosystem functioning and the species that reside within them. An imbalance in the protection of freshwater ecosystems, with significant underrepresentation of lowland freshwater ecosystems, makes these the most threatened ecosystems in New Zealand.2. Recent policy initiatives are attempting to take a whole-catchment view, i.e. 'from the mountains to the sea'. There is also an increased focus on the restoration of vulnerable water bodies that still support moderate values, in preference to previous long-term restoration programmes for the most degraded freshwater sites. The outcomes of these programmes have been less certain, with opportunities lost for systems that are declining in condition but have not yet reached the threshold of degradation for investment.3. This work demonstrates the gains that can be made through the use of spatial conservation prioritization software to identify priority catchments for freshwater restoration, emphasizing the representation of a full range of ecosystems and species, while also taking account of longitudinal-connectivity constraints within catchments.4. Third-order subcatchments were the most suitable scale for this prioritization, to capture the most important components within the largest river catchments. Populations of important native fish populations and the locations of major terrestrial conservation projects were also considered when assessing priorities; iteratively chosen weightings were applied to control the balance of representation across these different features.5. Consideration was also given to existing patterns of protection, in order to assess the biodiversity representation within areas currently protected and to identify sites that would provide maximum additional benefits if restored or protected.6. The resulting subcatchment prioritizations have contributed strongly to regional collaborative restoration processes.