Avian botulism poses a significant risk to waterbird health in Australian wetlands. This paralytic, often fatal, disease occurs when birds ingest a neurotoxin produced by the bacterium Clostridium botulinum. Our current understanding of avian botulism comes largely from studies in the northern hemisphere, with many of these studies linking outbreaks of avian botulism with poor water quality. The Murray–Darling Basin provides the most important breeding habitat for colonial waterbirds in Australia, but the frequency of large-scale breeding events has declined, and waterbird populations are near record-low numbers. Avian botulism has the capacity to have significant impacts on waterbird recruitment if not managed appropriately. We propose that environmental water-management strategies that aim to maintain water quality through flow delivery to waterbird colonies could mitigate the risk of botulism outbreaks and contribute to waterbird population recovery.