Changes in aquatic macrophyte populations in the Burnett River in southeast Queensland, Australia are described with respect to the effects of water level fluctuations and possible impact on the Queensland lungfish (Neoceratodus forsteri). This protected fish relies on macrophyte beds as spawning and nursery areas. Studies were conducted prior to, during and following construction of a new weir on the river. Comparative results of impounded and non-impounded sites were conducted to investigate seasonal and inter-annual changes in macrophytes and the effects of both a rapid rise in water level when the impoundment first filled and a decline, on new plants in shallow water. Macrophyte communities in newly inundated areas were studied to determine the time taken for seedlings to emerge and reach a cover sufficient to represent spawning habitats for the lungfish. Vallisneria nana dominated the macrophyte beds, which were scoured from the river by a large flow event in May 1998, the effects of which persisted for at least one year. Most newly emerging seedlings of Vallisneria perished following a small decline of 7 cm in water level. Decrease in plant biomass and death of established plants in highly turbid water resulted within 6 to 9 weeks following larger water level rises of 4.0 - 5.5 m in the new impoundment. In the period leading up to the lungfish spawning season at least five months is required for submerged plants to reach the 90% cover preferred for spawning. Implications of the results for water level management and lungfish populations are discussed.