The rivers and ecosystems of Australia’s Murray-Darling Basin are some of the most highly modified in the world. The estuary at the Basin’s terminus exemplifies these impacts. The plight of the Murray Estuary and Coorong lagoons, and the freshwater Lower Lakes (Alexandrina and Albert), were brought to prominence during the Millennium Drought from 2001-2010. During this time, the naturally perennial River Murray stopped flowing to the sea for 1280 days and 7-km of tidal barrages physically separated freshwater and estuarine environments, which became marine and hypersaline. The degradation of the estuarine ecosystem and associated fish populations was impetus for the region’s designation as an Icon Site under the Murray-Darling Basin Authorities’ The Living Murray Program, which included increasing delivery of water for the environment and interventions to improve connectivity (e.g. fishways). Since the early 2000’s, State and Commonwealth governments have supported a host of research projects in the region to understand the population dynamics and life histories of estuarine-associated fishes, and to assess response to management interventions. Here we present case studies on select diadromous (e.g. congolli, Pseudaphritis urvilli) and estuarine fishes (e.g. black bream, Acanthopagrus butcheri), and address the utility of research in informing the management of freshwater flow (including water for the environment) and actions to promote connectivity across the barrages. Despite advances in the management and conservation of fishes in the Coorong, future challenges include the impacts of a changing climate and associated decreases in river flow and increases in water temperature and sea-level. In light of these challenges, we consider alternative interventions to benefit the estuarine ecosystem and its fishes, including more permeable barrage operation to promote estuarine dynamism and greater hydrological and biological connectivity.