The protection of refuges has been proposed to offer means by which we can assist species and ecosystems to adapt to climate change. Refuges are places secure from one or more disturbances, from which individuals emerge to recolonise landscapes after disturbance has ceased. Refuge function relies on two ecological processes: disturbance and recolonization. Recolonization depends on species’ capacity for dispersal and reproduction to repopulate landscapes. Australian freshwater ecosystems are often disturbed by droughts, floods and wildfire, so freshwater species are expected to possess strategies for resisting or being resilient to disturbance. However, by altering basic environmental variables or increasing the frequency or intensity of disturbance, climate change presents new challenges to populations. Recent research shows that temperature and drought refuges exist across spatial scales in streams and wetlands. These refuges function to sustain biodiversity during single disturbance events, prolonged disturbance (e.g. millennium drought) and the onset of climatic drying (> 20 y of rainfall decline). In this keynote I explore a variety of refuges across spatial scales to demonstrate refuge function, which often relies on habitat features at the small scales relevant to individuals. Many species rely on microhabitat-scale refuges or on fringing vegetation for persistence and dispersal. Survival in refuges often involves specialized traits. Experiments that challenge species to respond can reveal previously undiscovered traits and unsuspected resistance capacity, potentially explaining unexpected biodiversity patterns, given climatic drying. Where humans alter freshwater ecosystems, such as through flow regulation and damage to fringing vegetation, connectivity and dispersal are reduced, compromising refuge function. Local extinction may occur and food webs may be modified, limiting adaptive capacity. Refuges will be key to the future viability of populations in fresh waters; but we need a much greater understanding of ecological processes across all life stages of species, especially those dependent upon, and vulnerable in, refuges.