This research investigates the challenges and opportunities of urban estuaries exposed to spatial, urban, and environmental shifts exacerbated by climate change, ecological disturbances, and population growth, taking the cities of Perth, Western Australia and Newcastle, New South Wales, as case studies. Approaching the design of estuary cities in the Climate Century demands a form of estuary urbanism and new paradigms in design, which embrace the constant presence of water. Water becomes the instrument of change to re-think the design of the city and its relationship with the non-built environment since the climate crisis is also a water crisis. Adaptation and mitigation strategies are still emerging fields in design and planning disciplines. Design disciplines can strongly contribute to generating site-specific climate-adaptative responses while re-establishing the connection between built and natural environments, improving ecological balance and spatial quality, and promoting well-being and cultural values. The methodology involves both analytical and projective-explorative methods promoting a site-specific approach, working across scales and disciplines to understand urban estuaries within larger catchments and as complex hydrological and ecological systems. A fundamental goal is the creation of site-specific design strategies to operate in low to medium-density precincts, leveraging water and nature as design tools to improve urban resilience and liveability. There is capacity here to establish design methods and principles that inform future practices through urbanism responding to dynamic ecological and water systems and the unpredictability effects of climate change.