Western Australia’s non-tidal waters provide refuges to many unique fishes. Here we provide an overview to synthesise contemporary knowledge on these species with the aim of providing readers with an understanding of their biological, ecological and conservation significance. Western Australian inland aquatic ecosystems provide critical habitats for many obligate freshwater fishes as well as diadromous species that rely on fresh water to complete their life-cycle. Five of Australia’s 10 ichthyological provinces are found within the State, three in their entirety. Notable species from evolutionary and biogeographic perspectives include the enigmatic Gondwanan relic Lepidogalaxias salamandroides (Salamanderfish) and the ancient jawless fish, the anadromous Geotria australis (Pouched Lamprey) in the Southwestern Province. The Pilbara Province supports Australia’s only known obligate vertebrate stygofauna, including one of the world’s largest stygofauna species, Ophisternon candidum (Blind Cave Eel), and two blind eleotrids (Milyeringa spp.). The freshwaters of the Kimberley region support three elasmobranchs including Pristis pristis (Largetooth or Freshwater Sawfish) and features high species richness and endemicity in the Terapontidae and Eleotridae. The Paleo Province encompasses much of the arid interior of the State, and has very few records of fishes. Western Australian rivers also provide habitat for a small number of euryhaline elasmobranchs that have become vulnerable to extinction elsewhere, and other fishes that utilise these habitats as nurseries. The State supports many fishes that are nationally and internationally listed as threatened or of conservation concern and an increasing number of alien fishes. We collated a total of 102 native fish species that are found within fresh waters of the State, of which 66 are obligate freshwater fish species, three are stygofauna, and a further two have amphidromous and potamodromous populations. In addition, several estuarine species are able to breed in fresh waters, the remainder being diadromous or ‘wanderers’ that are freshwater vagrants.