Euro-Mediterranean running water ecosystems represent a highly threatened habitat due to draining, construction, agriculture, eutrophication, pollution and climate changes. Thereby, the associated biodiversity is often more threatened compared to any other ecosystem and the identification of biodiversity hotspots and conservation priorities for running water fauna is therefore a primary target. Here we focused on invertebrates, as important indicators of ecosystem functions, modelling a lineage of water beetles and investigating the conservation status of Euro-Mediterranean headwater ecosystems. We selected the "Haenydra" lineage (Hydraenidae, genus Hydraena) as representative taxon (92 species overall, known to occur from Iberian Peninsula to W Iran), analysing a geographic database including literature, field-collecting and Museums data in order to map the distribution of biodiversity hotspots in Euro-Mediterranean headwater systems and locate the running water sites potentially important for invertebrates conservation. We hence assessed the conservation priorities assigning IUCN threat Categories-following IUCN guidelines-to all the species of the lineage, together with a herein introduced Conservation Score (CS) computed using a procedure tailored specifically for water beetles, also analysing historical series. We found that threatened categories (VU or higher), with high CSs, should be assigned to >70% of the species, suggesting that, considering this lineage a representative model, the headwaters conservation status in Euro-Mediterranean areas is alarming. Cantabria, Pyrenees, Alps and Central Apennines were identified as biodiversity hotspots, whereas the combination of IUCN categories and CSs revealed that the areas with highest conservation concern are distributed in W-Alps, E-Alps, Apennines, Central Spain, Greece and N-Turkey. Our analyses suggested a dramatic worsening of running water ecosystems in several Mediterranean regions and in particular in Italy, Greece and Turkey. The comparison between the IUCN categories and the newly introduced CSs evidenced the importance of taking into account the ecological, hydrogeological and historical features when assessing conservation strategies for running water organisms