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Addressing spatial connectivity in conservation planning is important to ensure the maintenance of patterns and processes needed to support the persistence of biodiversity. In freshwater ecosystems, spatial connectivity is constrained by the presence of water, which exhibits marked temporal changes in regions with wet-dry seasonal climates. Previous studies have focused on spatial connectivity and overlooked the temporal component, which is required for the functionality of spatial connections (because of temporal changes in water availability)., We identify priority areas for the conservation of freshwater fish, waterbirds and turtles in the Mitchell River catchment in the wet-dry tropics of northern Australia. We demonstrate how adequacy of freshwater conservation can be enhanced by integrating an estimate of water residency time ( WRT) into the prioritization process. WRT reflects refugial potential and connectivity in freshwater ecosystems and was quantified using Moderate Resolution Imaging Spectroradiometer ( MODIS) flood and post-flood Landsat satellite imagery. We compare the spatial allocation of priority areas and the spatial and temporal connectivity under two alternative scenarios: (i) accounting only for spatial connectivity and (ii) integrating spatial and temporal connectivity., Priority areas identified under the spatial and temporal connectivity scenario showed a 40% increase in WRT values with respect to the traditional spatial connectivity scenario. This was achieved at no additional cost in terms of total protected area and maintaining the same spatial connectivity., Despite priority areas identified under the two alternative scenarios showing intermediate spatial overlap (64%), the selection process was more efficiently biased towards planning units with high WRT values. WRT in planning units that were only selected under the temporal connectivity scenario was 2·5 times higher than in planning units that only appeared in the traditional connectivity scenario. This reveals the importance of accounting for WRT when identifying freshwater priority areas in wet-dry seasonal environments., Synthesis and applications: Considering the temporal connectivity in conservation prioritization as we propose here helps to assess periods of longest spatial connections, thereby maximizing the refugial role of freshwater priority areas during dry periods. Using publicly available satellite imagery data and software, our approach allows improved management of aquatic resources and biodiversity during periods of water scarcity, which may increase in incidence and duration with climate change. [ABSTRACT FROM AUTHOR]