The implementation of the belt and road initiative (BRI) in Central Asia, home to one of the 36 Biodiversity Hotspots, poses socioecological challenges to local groundwater-dependent ecosystems (GDEs), potentially hindering progress of the Global Biodiversity Framework (GBF). Urgent GDE conservation is therefore critical to align the interests of the BRI and GBF. Using a newly released high-resolution global GDE dataset, we analyzed the spatial distribution pattern, protection status, and conservation priorities of GDEs across Central Asia. The region hosts more than one-third of the worldwide dryland GDEs, with Kazakhstan alone accounting for 13.4% of the total and covering 42.1% of its territory. Yet the representation of protected GDEs (GDEs within protected areas) remains critically low (Jacob's index < 0), particularly under strict protection levels. In Biodiversity Hotspots, this shortfall is even more pronounced (Jacob's index approximate to -1). Spatial prioritization identified potential protected areas mainly in Kazakhstan (37.5%), China (28.8%), Mongolia (17.9%), and Uzbekistan (7.9%). In Central Asian Hotspots, implementing these priorities could raise protection coverage to 25.8%. These findings underscore the urgent need for conservation efforts targeting GDEs in Central Asia. Such efforts are essential to harmonize the goals of the BRI with the ambitions of the GBF, facilitating mutual progress rather than conflict between development and biodiversity conservation.