Fisheries research, assessment and management is increasingly challenged by a need to broaden the previously narrow biological focus through consideration of ecosystem and habitat protection, biodiversity conservation, economic targets and social outcomes to support decision-making for sustainable management.  These multiple objectives are further complicated by the need to account for the impacts of global climate change. In this talk I provide an overview of some modelling and related tools that are being used to address the increasing complexity and global connectedness of fisheries systems as well as account for changing targets and baselines. Examples are drawn from the Torres Strait tropical lobster and sea cucumber fisheries, Northern Prawn Fishery, forage fisheries and management of the crown of thorns starfish on the Great Barrier Reef. These examples highlight how management can effectively guide science to collectively address the key issues in fish and fisheries management. As an example of including socio-economic dimensions into ecological research and management frameworks, I provide an example of how socio-ecological models are being extended to represent dynamically the two-way feedbacks between ecological systems and linked socio-economic systems. In addition, I discuss the need to develop pre-tested strategies and adaptation options to prepare for climate change and respond appropriately to changes in the state and organisation of ecosystems, and their dependent societies. Finally, examples are provided of the challenges of facilitating communication with diverse stakeholders given that the success of future sustainability initiatives depends critically on effective communication.