1. Fresh waters and their resources continue to be one of the most imperilled ecosystems on Earth, yet very little emphasis has been placed on identifying and developing in situ conservation mechanisms, such as freshwater protected areas. In the southern region of the Western Ghats Hotspot, India, a globally important eco-region harbouring unique freshwater taxa, there has been very little effort to identify the role played by terrestrial protected areas in freshwater biodiversity conservation.2. Around 130 species of freshwater-dependent fauna belonging to five taxonomic groups (fish, amphibians, crabs, shrimps and odonates) are endemic to the region, of which 25% have a high risk of extinction. More than half of the 130 species are not represented in the current protected area (PA) network, and the distributions of 12 endemic and threatened species (10 fish, one amphibian and one shrimp), of which five are single-location species, also fall wholly outside the PA network.3. Although 44% (58 species) of endemic freshwater-dependent fauna of the region occur either wholly (25 species) or partly (33 species) inside terrestrial PAs, they are rarely subject to species-specific management or monitoring plans.4. To improve freshwater biodiversity conservation at the local level, and to achieve global conservation targets, such as the Convention on Biological Diversity's Aichi targets (for example targets 11 and 12), the PA network of the region should be doubled. This may be achieved by expanding the area of existing PAs to incorporate priority sites for freshwater taxa, creating new PAs by specifically targeting areas that are of significance to freshwater biodiversity, and developing and implementing freshwater-specific management plans in existing PAs of the region.