Developing and implementing effective adaptation policies for freshwater and estuarine systems in Australia will be a significant challenge in a rapidly changing climate. The broad aims of climate change adaptation policies are to reduce vulnerability and increase the adaptive capacity and resilience of ecosystems to climate change impacts. There are a range of adaptation policy options relevant to aquatic systems, and many of these measures can be 'mainstreamed' or incorporated into existing conservation and resource management frameworks. This article evaluates adaptation policy options and the constraints on policy implementation for freshwater and estuarine ecosystems in the coastal floodplains of tropical Queensland. Many of these aquatic systems are in a degraded condition and are vulnerable to the compounded impacts of climate change and other stressors. The analysis suggests that statutory planning schemes, water resource planning and protected area frameworks provide limited scope to address the more severe threats to these systems from rising sea levels, extreme cyclones, floods and droughts. In many locations, the effectiveness of adaptation policies is constrained by existing land uses and competing demands from communities and industry sectors. To prevent further widespread loss of habitat may require the development and implementation of new policies that prioritise adaptation management for freshwater and estuarine ecosystems. Keywords: climate change, adaptation policies, rivers, wetland ecosystems