Finding the balance between species water requirements and maintaining water security is challenging for water managers. We provide a case study about the science that has led to improved water resource management and targeted environmental flow strategies for Australian lungfish. This threatened and iconic species was prioritised for assessment based on previous studies suggesting a critical link between spawning and riverine flows/aquatic macrophytes. A 6-year monitoring and research project was undertaken in the Burnett River, Queensland, which focused on hydraulic habitat requirements for the species and impacts of water impoundments. Firstly, the study investigated the role of stream flow in riverine and impounded habitats, and its effects on lungfish spawning (where eggs were collected using push nets). Lungfish spawning was found to be a seasonal strategy, reliant on variable low-flow and dense macrophyte, within shallow riverine habitat¹. Having established these requirements, the second part of the study investigated spawning habitat availability in riverine and impounded reaches subject to current water management. Impoundment operation was found to substantially decrease the availability of spawning habitat for lungfish as water level fluctuations led to inundation/desiccation of aquatic macrophytes. However, irrigation releases from dams were found to be of a suitable magnitude to cue spawning. Finally, the study assessed the effectiveness of current water resource management and proposed alternative strategies for ecologically sustainable development. Redirecting the focus of management from storage operations, to providing releases for the downstream environment was a key recommendation which culminated in legislated revised environmental flow strategies.