The south-eastern waters of Australia are predicted to be the most vulnerable area to global change, due to changes in East Australian, Leeuwin and Flinders Currents and associated increases in water temperatures; modification of local ocean processes, like coastal upwelling; sea-level rise driven threats to inshore habitats, which have critical fish nursery roles; and other threats to inshore habitats posed by simultaneous increases in salinity, river flow and stratification of shallow water bodies. Together these shifts will impact species composition of functional groups and communities in the region. Moreover it will affect the sustainability of the fisheries (commercial and recreational) and aquaculture resources, which will have social and economic flow-on effects for the businesses and communities; particularly as they will be exacerbated by changes in market conditions, input costs and food prices as global change affects consumer purchasing behaviour changes. This means there is a strong need for information that casts light on exposure and vulnerability of the region and identifies robust management and adaptation strategies. Major benefits will only be achieved if there is a means of synthesising information across all topics (ecological, economic and social) to provide system level quantitative assessments and insights. This requires a method that can easily address changing socially and economically driven human behaviour, environments, ecological components, productivity and distributions and cross-jurisdictional human activities and management. Atlantis is uniquely placed in that it can directly address all of these critical factors. The SEAP program can also benefit from the years of development that have resulted in a working Atlantis model for the SE region.