Climate change presents significant challenges to modelling and managing aquatic resources. Equilibrium assumptions common in many modelling approaches need to be replaced by formulations that allow for changing baselines and integration of ongoing changes and adaptations by species, ecosystems and humans. As ecosystems change, so will the ways humans use, monitor and manage them. Consequently, adaptive management loops and supporting tools deserve more prominence in the management toolbox. Models are critical tools for providing an early understanding of the challenges to be faced by integrating observations and examining possible solutions. We review modelling tools currently available to incorporate the effect of climate change on marine and freshwater ecosystems, and the implications for management of natural resources. System non-linearity can confound interpretations and hence adaptive management responses are needed that are robust to unexpected outcomes. An improvement in the ability to model the effects of climate change from a social and economic perspective is necessary. The outputs from ‘end-to-end’ and socio-ecological models can potentially inform planning, in both Australia and the Pacific region, about how best to build resilience to climate change. In this context, the importance of well directed data-collection programs is also emphasised. Lessons from this region, which is advanced with regard to modelling approaches, can guide increased use of models to test options for managing aquatic resources worldwide.