Acid wetlands of wallum and dune systems in coastal eastern Australia are critical habitat for multiple threatened fish and frog species. Much of this habitat was recently affected by severe drought and wildfires. The extent of aquatic habitat degradation and impacts on threatened species populations is poorly understood. Prompted by the potential localised extinctions of species we know little about, we conducted surveys of the distribution and abundance of freshwater fish and frogs in more than 100 eastern Australian wallum wetlands, investigating the extent and severity of threats to habitats and populations. The study focussed on three species of fish and four species of frog of conservation concern that inhabit wallum wetlands: Oxleyan pygmy perch (Nannoperca oxleyana), honey blue-eye (Pseudomugil mellis), ornate rainbowfish (Rhadinocentrus ornatus), wallum froglet (Crinia tinnula), wallum sedgefrog (Litoria olongburensis), Cooloola sedgefrog (Litoria cooloolensis), wallum rocketfrog (Litoria freycineti). Our results provide up to date information on the distribution and population status of these fish and frog species, including discovery of new populations for several species. Alien fish species (Poeciliidae) were widespread, occurring at over 1/3 of survey sites and were considerably more prevalent at fire affected sites than native species. A number of localised extinctions occurred at heavily burned sites, however these sites were also subject to extended periods of drought, possibly drying before the fires. While the direct impact of fire alone was likely minimal at most locations surveyed, it is difficult to disentangle the concurrent and likely compounding effects of other stressors, including drought, riparian degradation, and invasive species. This project has established an updated baseline for future monitoring of freshwater fish and frogs, habitats and threats in coastal wallum ecosystems.