Terrestrial protected areas are often designated in inaccessible high elevation regions, and usually targeted towards conservation of charismatic large mammals and birds. It has been suggested that such protected areas, with partial coverage of riverine habitats, may not be adequate for conservation of freshwater taxa such as fishes. Also, protected areas are often designated in upstream catchments of dam reservoirs, and conservation of freshwater biodiversity is usually not a priority. We investigated the importance of existing protected areas for conservation of stream fishes within and across three dammed and two undammed rivers in the southern Western Ghats, India (a global biodiversity hotspot). Comparisons of stream sites in protected and unprotected areas were restricted to mid elevations because of confounding factors of dams, elevation and stream order. For dammed rivers, endemic and total species richness was significantly higher inside protected areas than unprotected areas. Total fish species richness increased with decreasing elevation and endemic species richness peaked at mid elevations. Species found in comparable stream orders across dammed and undammed midland river reaches were similar. Intensity of threats such as sand mining, dynamite fishing, pollution and introduced invasive fishes was higher in unprotected than in protected areas. Lack of awareness among managers has also led to the occurrence of some threats within protected areas. However, existing protected areas are vital for conservation of endemic fishes. Our results support the need for extending the scope of terrestrial protected areas towards better representation of freshwater ecosystems and biodiversity.