Freshwater ecosystems and the biodiversity they support are integral parts of the environment. Anthropogenic impacts on freshwater ecosystems have caused widespread declines in populations that depend on the habitat for breeding and feeding. Many waterbirds, such as ibis and spoonbills, rely on water in wetlands for such habitat. Changes to wetland water regimes can result in fewer breeding events, reduced breeding success (including nest abandonment) and starvation. However, the likely impacts of these changes on population trajectories and extinction risks have not been well quantified or modelled to-date. In this study, age-classed matrix population models were constructed for straw-necked ibis (Threskiornis spinicollis) and royal spoonbill (Platalea regia). These were built using vital rates obtained from a synthesis of published and unpublished data, and used to show population trajectories for the study species in eastern Australia under various scenarios. The analyses express how sensitive the results are to changes in demographic parameter values. The results increase our understanding of potential waterbird population trajectories, and what factors are likely to have the greatest impact on populations. The new knowledge may be applied to inform conservation management of waterbirds in the Murray-Darling Basin, thereby improving the effectiveness of environmental water management in the Basin.