Moreton Bay and its associated estuaries are an example of a complex aquatic system that is under increasing pressure from rapid population growth and urbanisation. Although the extent of decline in ecosystem health within Moreton Bay and its associated estuaries is significant and well documented, a range of innovative management responses have been implemented to reverse current declines. An overview of the development of Moreton Bay is provided, highlighting the dynamic and resilient nature of the system over geological time. The ecological responses that occur at decadal timeframes are presented along with a summary of the current state of the Bay's ecology. The future challenges that are posed by predicted population increases, urbanisation and changes to the region's climate are also discussed. The highly variable nature of the system over relatively short timeframes (i.e. flood vs non-flood conditions) as well as the ability of the system to adapt to long term changes (i.e. past morphological and ecosystem shifts) suggests that Moreton Bay and its associated estuaries have significant capacity to adapt to change. Whether the current rate of anthropogenically induced change is too rapid for the system to adapt, or whether such adaptions will be undesirable, is unable to be ascertained in any detail at this stage. Notwithstanding the above, the combination of a science-based management framework and the collaborative decision making processes that have been implemented to halt the decline of Moreton Bay have shown remarkable progress in a relatively short period of time.