Aquatic macrophytes are vital for the survival and recruitment of the Australian Lungfish (Neoceratodus forsteri) offering feeding, breeding, and juvenile nursery habitats. Macrophytes are impacted by numerous threats, including major droughts and flooding events that desiccate and scour macrophytes from rivers. The Brisbane River in south-eastern Queensland, is home to a large population of lungfish, and is punctuated by a large water supply and flood control reservoir that alters the hydrology of the river, providing ideal conditions for dense macrophyte growth under normal operating conditions. In 2011, a major flood event completely scoured macrophytes from the main trunk of the river. Upstream of the dam, macrophytes recovered well after 3-4 years, whereas below the dam, recovery is largely absent 13 years since the flood. Given the extreme longevity of Lungfish, Population Viability Modelling has assisted to contextualise the potential impact of this situation over the long term. Active macrophyte rehabilitation has been trialed to enhance recovery rates below the reservoir. While effective rehabilitation is yet to be achieved, the research has revealed many new insights into macrophyte dynamics, active rehabilitation efforts, unforeseen challenges from lungfish themselves, and the criticality of healthy macrophyte habitats for Lungfish across their range.