Biodiversity conservation across countries and ecosystems is traditionally based on a single species- or area-level attributes, such as endemicity or taxonomic diversity. Although alternative criteria integrating multiple biodiversity aspects on both species- and area-level have been proposed, they are only rarely considered in conservation planning, especially in data-deficient ecosystems. Among them are also groundwater ecosystems, which are almost exclusively protected only indirectly through protected areas (PAs) targeted at surface ecosystems. Due to their interdependency, surface PAs can be beneficial for groundwaters, but it is unclear whether and to what extent they capture different aspects of groundwater diversity. We addressed these questions at the subterranean biodiversity hotspot, the Western Balkans (Europe), using amphipod family Niphargidae as a model system. We integrated distributional, phylogenetic, and functional trait data for over 200 molecular operational taxonomic units (MOTU). We explored the patterns of different biodiversity facets and identified MOTUs and areas of highest conservation importance. We evaluated how well do PAs overlap with high-priority MOTUs and areas, and how much regional diversity PAs capture with their extent. Over a third of high-priority MOTUs were distributed outside PAs, while <30 % of high-priority areas had over half of the area overlapping with PAs. Additionally, we found that over 30 % high-priority MOTUs were formally undescribed species. Although existing PAs only poorly covered the high-priority MOTUs and areas, they still captured over 50 % of each diversity facet in the region. Finally, we list the next steps to improve the conservation strategies of groundwater ecosystems in Europe.