We review interactions between waterfowl and wetlands and outline the shifts that are likely to occur within these relationships through global climate change. We highlight the relative paucity of research on populations of tropical waterfowl and their food plants, and use an iconic tropical species of waterfowl, the Magpie Goose (Anseranas semipalmata), as a case study. We provide background on the known and hypothesised interactions between Magpie Geese and wetlands and provide a hypothetical framework of the mechanistic changes to these relationships through climatic change, including rises in sea level, temperature increases, elevated CO₂ levels and altered rainfall regimes. Intrusion of saline water through sea-level rise and extended periods of inundation following increased annual rainfall are the two plausible drivers of change in the wetland sedge plants that support Magpie Geese populations. We show how the relative importance of these, and other, threatening factors can be challenged with data from the field and laboratory under multiple working hypotheses. Understanding the imminent shifts in the structure of wetland plant communities and the likely response of waterfowl populations will focus management on key threats and critical habitat. This includes identification of important wetlands and the construction of buffers at them to slow salt-water intrusion.