In drying landscapes, drought refuges and evolutionary refugia are expected to become critical for conserving freshwater biodiversity. Southwestern Australia (SWA) has already experienced widespread loss of perennial streams due to climatic drying. We characterised drought refuges in formerly-perennial streams in a forested headwater catchment impacted by severe drying, where most streams are now intermittent, to determine their contribution to species persistence in the landscape and community recovery. Refuges sampled included small spring-fed pools, perched receding pools and subterranean refuges associated with granite inselbergs; no hyporheos was present. Dry substrata were collected from each intermittent stream for rehydration, and a subsample were aerated to break dormancy in species that require flow. Refuge types had very different invertebrate assemblages: spring-fed refuges supported several locally-endemic species, but perched pools were dominated by opportunistic colonists. Taxa were found aestivating in dry sediments, primarily adult Coleoptera and larval Chironomidae. Inselberg springs supported small populations of endemic Trichoptera and Ephemeroptera and are a potential subterranean evolutionary refugium for an endemic paramelitid amphipod. Despite the diversity of species found, dry season refuges did not significantly contribute to community recovery. Instead, recolonisation from perennial streams was likely the primary process of community recovery. Drought refuges did allow a few locally-endemic species to persist, however, the existence of these refuges is also under threat from intensifying climatic drying. Continued loss of perennial streams in SWA will result in landscape wide reductions in local diversity as colonisation sources for intermittent streams are lost, because there are no known evolutionary refugia present in this landscape for relictual species to retreat into. Thus, identification and protection of future evolutionary refugia is a matter of urgency in regions facing drier climates, as it is ultimately evolutionary refugia that will become critical reservoirs of freshwater biodiversity as perennial streams and refuges are lost.