South-western Australia has had a drying climate for 40 years and is getting drier. In the Perth region, large declines in hydroperiod have occurred and few perennial waterbodies remain, so that, in headwaters, conservation managers cannot prevent drying or the consequent extirpation of freshwater species. However, perennial waters do still occur frequently in this landscape, but lie on private land in farm dams. This study sampled freshwater biota (plants, invertebrates, tadpoles) in perennial farm dams (>50 dams) and natural streams and wetlands (>40 sites) in the Perth region in spring and autumn. Stands of native submerged plants were common in farm dams and were associated with higher invertebrate species richness. Unsurprisingly, suspension-feeding invertebrates were absent from farm dams, but most other invertebrate taxa occurred at least in some locations. Dams varied widely in invertebrate richness and composition; but some supported diversity comparable to natural waterbodies. They also contained species that have no life history stage tolerant of drying, which are now absent from most natural waterbodies (e.g. Palaemon australis). Tadpoles were present in dams, but burrow-nesting species were less common than others. Perennial farm dams in this region have the capacity to support native species and most native species will use them as habitat. Their high frequency in the landscape means that if even a small proportion of dams were managed to improve their function as refuges, they could contribute to preventing extirpations in this region. The next stage of this research is to investigate appropriate management tools to improve refuge capacity and function. Conservation of freshwater species will increasingly depend on managing all the freshwater in this landscape, regardless of where that water might be.