Platypus inhabit several streams across the greater Melbourne area, although historical records and long-term live trapping surveys since 1995 indicate several populations are contracting in their distribution and declining in abundance. Regional conservation requires identification of threats and opportunities to prevent further declines, particularly in the context of predicted human population growth and changes in climate in the coming decades. We developed and applied spatially explicit, quantitative habitat suitability models to understand the potential impacts of urban growth and climate change on Melbourne’s platypus populations and to identify the combination of management actions that is most likely to maintain or improve populations over the next 50 years. Reliable platypus habitat suitability models were developed and their performance was assessed both quantitatively and qualitatively, including validation using an independent eDNA dataset. Extensive reductions in suitable platypus habitat are predicted to occur over the next 50 years, with the greatest threat being a drier future. Platypus populations are likely to become extinct in all but two river systems in Melbourne within 50 years if streamflow is reduced by the magnitude predicted by current climate change models. In addition to revegetation and urban stormwater management, a critical requirement for maintaining platypus populations throughout the region will be the provision of adequate flows in areas of favourable habitat. This project is an example of how spatially-explicit quantitative habitat modelling and a whole-of-landscape approach can help us strategically understand threats and identify actions to ensure platypus persistence within urbanising settings.