We examine the impediments to scientific integrity with an analysis of the water science-policy interface for the Murray-Darling Basin (MDB), Australia. We highlight the dangers to the public interest of â€˜administrative captureâ€™ of science, whereby scientists are incentivised to narrow or close down the scientific questions asked, the debates on evidence and the scientific dialogue so to support predetermined policy actions. Administrative capture of science is not intended to be objective or disinterested and contributes to a diminution of trust in science and scientists. Using an integrative theoretical framework for analysis of the different stances taken by scientists in scienceâ€“policy interactions, we show how scientists as Issue Advocates have sought to limit debate and the options available in relation to water reform in the MDB. We provide six possible actions to reduce administrative capture that encourages scientists to become Issue Advocates. These actions include procedural, professional, evaluative, judicial, instrumental and external controls that support scientific integrity by individuals and agencies that use and/or undertake publicly funded research.