While ecological theory informs us of the importance of scale in managing fish populations, the links between such theories, and the realities of managing for biodiversity outcomes can become tenuous. Australia is the world’s driest inhabited continent, and in our largest and most productive water catchment the Murray Darling Basin Plan (2012) is being implemented in an attempt to strike a balance between the need for agricultural and environmental outcomes. These links between theory and reality have been tested and retested as managers, farmers, scientists and politicians grapple with getting the most from a limited resource. While agricultural outputs are easily measured, quantifying the outcomes of restoration of fish species that have life-history processes which can span huge spatial and temporal scales, in a way that is politically palatable, is hard. Under this context, breakthroughs in scientific and social understanding have progressed our knowledge and management of MDB fish. Here we demonstrate the changes in management of key fishery resources over recent (<250 years) history using several case studies of unique management approaches. We also discuss the social and political aspects of undertaking such management at large scales, and provide an Australian perspective on operationalising conservation planning.