1. Freshwater ecosystems are amongst the most threatened and poorly protected globally. They continue to be degraded through habitat loss, pollution and invading species and conservation measures are urgently needed to halt declining trends in their biodiversity and integrity.
2. During the past decade a suite of decision support tools and computational approaches have been developed for efficient and targeted conservation action in terrestrial or marine ecosystems. These methods may be poorly suited for planning in freshwater systems because connectivity in terrestrial and marine systems is typically modelled in a way unsuitable for rivers, where connectivity has a strong directional component.
3. We modify the conservation prioritization method and software, zonation, to account for connectivity in a manner better suited to freshwater ecosystems. Prioritization was performed using subcatchment/catchment-based planning units and connectivity was modified to have directional upstream and downstream components consistent with the ecology of our target species.
4. We demonstrate this modified method for rivers and streams in the southern North Island of New Zealand. Data included predicted occupancy from boosted regression tree models of species distributions for 18 fish species. The study area covered 2.1 million hectares and included 394 first- to fourth order catchment or subcatchment planning units.
5. Realistic modelling of connectivity had a major influence on the areas proposed for conservation. If connectivity was ignored, recommended conservation areas were very fragmented. By contrast, when connectivity was modelled, high priority conservation targets consisted of entire river basins or headwater subcatchments.
6. The proposed method serves as a starting point for the implementation of reserve selection methods in river ecosystems.