The Mary River (Moonaboola) in Queensland is a hotspot of threatened aquatic species, including the endemic Mary River cod. The last extensive surveys of this river system occurred ~30 years ago, resulting in a limited understanding of the species’ current distribution and population trends. Since then, extreme weather events have caused sequential severe droughts, heat waves, wildfires and floods. Coupled with habitat degradation and invasive species, these interacting threats pose increasing risks to the resilience and long-term survival of the Endangered Mary River cod. In this study, we established a post-impact baseline for the present distribution and demographics of Mary River cod and interacting species within the Mary River. We also trialled nesting habitat enhancement using naturally occurring materials. Mary River cod were limited and fragmented in their range compared to historic data, and low in abundance. Contrary to cod, introduced fish species were abundant, and have substantially increased from their historic distributions. While several concerning trends were recorded by this study, it is difficult to disentangle the concurrent and likely compounding effects of extreme events, riparian degradation and invasive species. Information gained from this study is being used to guide future recovery actions for the species and their habitat.