Scientists have played a pivotal role in the identification of ecological problems, management and protection of rivers in Australia. Perhaps because of this, science has sometimes come under attack. Like climate change science, river science is also increasingly the focus for criticism for providing the ‘wrong’ answers for major public policy decisions. This attack is particularly conspicuous on the science of the Murray-Darling Basin rivers, our most developed major river basin. The building of large dams primarily for hydroelectricity generation and supply for irrigation and urban water has incurred major ecological and social costs to the rivers and wetlands of the Murray-Darling Basin. Recognition of the poor ecological state of many rivers and wetlands led Australian Governments to invest >$12 billion in the rehabilitation of the Murray-Darling Basin Rivers, including the return of environmental flows. The volume of this environmental flow target has continued to decline with powerful stakeholder pressure, particularly from the irrigation industry, persuasively arguing about significant socio-economic impact. At the same time, rivers of northern Australia are now the ‘new frontier’ for development, with considerable investment of public resources. Science remains pivotal to the success of the Murray-Darling Basin Plan but implementation mechanisms need a serious overhaul. Scientific effort also needs to be driven by management objectives, which are rarely adequately specified. Science also needs to deliver ‘real-time’ data for management, not just ‘the paper’, more than three years later. Finally scientists need to continue to ‘stand-up’ publicly for Australian rivers and ecosystems, whether providing evidence for improved implementation of environmental flow management or protection of free-flowing rivers in the Lake Eyre Basin and tropical Australia. We can’t afford to make the same mistakes on our other river systems.