State and federal governments in Australia recently approved water management plans for one of the largest coal mines ever proposed. This comes as the role of coal in the world’s future energy mix is being seriously questioned, and global concern over the climate and water implications of further fossil fuel development. Despite repeated advice from multiple independent scientists, governments did not compel the mining company to conduct the investigations required to determine its risks to important nearby groundwater-dependent ecosystems, leaving open the prospect of irreversible ecological and cultural damage. Here we show how scientific advice provided to decision makers was repeatedly ignored or dismissed, while scientists and agencies were subjected to political pressure. We argue that this echoes other examples of scientific evidence being ignored where findings clash with political or economic objectives, and warrants urgent review of decision-making processes for developments with major environmental consequences.