Abstract Range size is one of the most important criteria for determining species conservation status. It is an outcome of multiple factors, including a species' ecological tolerance and propensity to disperse, availability and temporal stability of suitable habitat patches, and between‐patch connectivity. Understanding the determinants of range size could help identify the main threats, which may differ among species. Subterranean species typically have smaller ranges than their surface counterparts. However, the determinants of their ranges are poorly known. The aim of this study was to test three potential determinants of species range size (habitat type, body size, and species age) using the species of the amphipod genus Niphargus. The study was performed within the Dinarides (south‐east Europe), a global subterranean hotspot. The only significant determinant of range size was the habitat in which the species lived. The species with the smallest ranges inhabit fissure systems in the upper layers of the carbonate massifs with predominantly vertical water flow. The species with the largest ranges live in the deepest zone – the permanently flooded phreatic with lateral water flow. These results imply that differences in connectivity among habitats determine the range sizes of aquatic subterranean species. The vertical gradient in habitat connectivity indicates the vulnerability of the species to climate change. Desertification and longer periods of drought will probably have a greater effect on fauna in fissures than in the phreatic zone. In addition, lowering the groundwater table might exacerbate the fragmentation of intermediate habitats, possibly enhancing local extinction. The habitat ecology of subterranean species should be considered in International Union for Conservation of Nature assessments. Given that the most narrowly distributed aquatic subterranean species live in habitats subjected to climatic drying, the protection of subterranean fauna depends on the management of surface habitats such as forests.