1. River systems have strong linear linkages. Innovative solutions to capture these linkages are required from aquatic conservation planners.
2. We apply an approach to freshwater conservation planning to freshwater ecosystems of KwaZulu-Natal (South Africa), using generic conservation planning software. We used a two-step, hierarchical process to capture catchment- and local-scale dynamics, where priority primary catchments were first identified and then used at a second level for selecting priority subcatchments, which served as planning units at a finer scale.
3. We set quantitative targets for defined freshwater biodiversity features. Priority planning units at both catchment levels were selected using modified weighted cost discounts and penalties, which included the presence of priority estuaries and free-flowing rivers, planning units falling within priority primary catchments, planning units identified as important in an existing terrestrial conservation plan and the degree of catchment degradation. Ecological processes were incorporated by discounting planning units important for surface and groundwater yield.
4. Upstream–downstream connectivity was achieved by linking adjoining subcatchments associated with main rivers and wetlands and enhanced by setting high targets for subcatchments through which eels (Anguilla mossambica) must migrate.
5. The hierarchical approach of selecting priority primary catchments and using these to affect subcatchment costs, plus the use of high targets for migratory fish species, is applicable to any freshwater conservation plan to favour planning unit selection within selected basins, while facilitating connectivity in upstream–downstream subcatchments.