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Climate change has intensified the effects of habitat fragmentation in many ecosystems, particularly exacerbated in riparian habitats. Therefore, there is an urgent need to identify keystone connectivity spots to ensure long-term conservation and sustainable management of riparian systems as they play a crucial role for landscape connectivity. This paper aims to identify critical areas for connectivity under two contrasting climate change scenarios (RCP 4.5 and RCP 8.5 models) for the years 2030, 2050 and 2100 and to group these critical areas by similar connectivity in keystone spots for sustainable management. A set of analyses comprising climate analysis, drainage network analysis, configuration of potential riparian habitats, riparian habitat connectivity, data clustering, and statistical analysis within a Spanish river basin (NW Spain) were applied. The node and link connectivity would be reduced under the two climate change scenarios (≈2.5 % and 4.4 % reduction, respectively), intensifying riparian habitat fragmentation. Furthermore, 51 different clusters (critical areas) were obtained and classified in five classes (keystone spots) with similar connectivity across the different scenarios of climate change. Each keystone spot obtained by hierarchical classification was associated with one or more climate scenarios. One of these keystone spots was especially susceptible to the worst climate change scenario. Key riparian connectivity spots will be crucial for the management and restoration of highly threatened riparian systems and to ensure long-term biodiversity conservation. • Connectivity importance was reduced under different climate change scenarios. • Critical area detection for connectivity conservation is threatened by climate change. • Critical areas were classified with similar connectivity keystone spots against climate change. • Keystone spots with high PC index will be priority for conservation management. [ABSTRACT FROM AUTHOR]