Australian marine systems are undergoing rapid environmental change, with some of the largest climate-driven changes in the Southern Hemisphere. While rapid change is predicted to continue, the magnitude will differ around Australia, as will flow-on effects on local communities and fishing businesses. We will describe recent multi-decadal ecosystem model projections for major fish stocks around Australia. For some fisheries, responses by fished species included both increases and decreases, indicating the potential for switching focal species. In the tropics, large fish stock changes can occur despite small climate changes due to non-linear influences on primary productivity supporting the foodweb. Fishing sectors and managers will need to be flexible if they are to cope with these changes and avoid the worst consequences. Management that is coordinated across State and Commonwealth fisheries and that links with other users of marine waters offers advantages. Healthy fisheries will also require information services that are updated regularly with the latest understanding of what Australia’s climate, fish, ecosystems and fisheries are doing. Such information should highlight those species that may be at risk, those that might benefit, and what actions are needed to mitigate undesirable outcomes and make the most of any new opportunities.