Acid wetlands of coastal wallum and dune systems are critical habitat for multiple threatened fish 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, given the last extensive surveys of these systems occurred more than 30 years ago. Prompted by the potential localised extinctions of species we know little about (Oxleyan pygmy perch and honey blue-eye), we conducted surveys of the distribution and abundance of freshwater fish in more than 100 eastern Australian wallum wetlands, investigating the extent and severity of threats to habitats and populations. Our results provide up to date information on the distribution and population status of several fish species of conservation concern and expand the known range of several others. 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, habitats and threats in coastal wallum ecosystems.