Many water scientists aim for their work to inform water policy and management, and in pursuit of this objective, they often work alongside government water agencies to ensure their research is relevant, timely and communicated effectively. A paper in this issue, examining 'Science integrity, public policy and water governance in the Murray-Darling Basin, Australia’, suggests that a large group of scientists, who work on water management in the Murray-Darling Basin (MDB) including the Basin Plan, have been subject to possible ‘administrative capture'. Specifically, it is suggested that they have advocated for policies favoured by government agencies with the objective of gaining personal benefit, such as increased research funding. We examine evidence for this claim and conclude that it is not justified. The efforts of scientists working alongside government water agencies appear to have been misinterpreted as possible administrative capture. Although unsubstantiated, this claim does indicate that the science used in basin water planning is increasingly caught up in the politics of water management. We suggest actions to improve science-policy engagement in basin planning, to promote constructive debate over contested views and avoid the over-politicisation of basin science.