We develop a high-resolution conservation prioritization analysis for New Zealand's rivers and streams that simultaneously consider both the present state (representation) of ecosystems, and the prioritization of management actions designed to mitigate ongoing human impacts on their expected future state (retention). As input we used information about the geographic distributions of river ecosystem groups and their compositional similarity, species richness, present condition as compared to their estimated pristine state, and upstream and downstream connectivity. Candidate management actions included riparian planting, establishment of wetlands on tile-drain outflows, and use of riparian buffer strips in plantation forests. The analysis, carried out at a 1-ha resolution for a study area of 22,000 km2 in Southland, New Zealand, demonstrates a credible range of options for management intervention, particularly in lowland streams under serious threat from agricultural intensification. The proposed analysis can be replicated elsewhere for terrestrial, freshwater, or marine systems using publicly available software.