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Freshwater ecosystems are among the most threatened worldwide. A great part of this threat comes from climate and land cover changes. This situation is specially worrying in areas and ecosystems that are highly relevant in terms of biodiversity but severely impacted by these two factors, such as water bodies in North Africa. Using water beetles as surrogates of freshwater biodiversity, we present a novel approach to identify priority basins for the preservation of freshwater biodiversity in Morocco, using Species Distribution Models to identify potential biodiversity hotspots under future climate change scenarios, and estimates of future Land Cover dynamics. The mountainous areas of the Rif and Prerif, Middle Atlas and northern Central Plateau areas, as well as some Atlantic coastal basins were identified as priority areas for water beetles conservation and will play a crucial role for the conservation of freshwater biodiversity. Indeed, these areas can act as a dead end for a number of African species in the future. However, most of these areas are poorly covered by the national protected areas network (i.e., protected area extent < 10%). In addition, our analyses revealed a general negative trend of the natural vegetation coverage in the study area, and an increase of non-irrigated cropland. Finally, we identified specific areas that need special attention because are priority for conservation but are expected to suffer intense land cover changes. These results, which consider not only biodiversity values, but also the potential threats driven by climate and land cover changes, can provide a solid scientific basis to policy-makers to define specific conservation measures to anticipate freshwater biodiversity loss in North Africa. [ABSTRACT FROM AUTHOR]