Although science is generally assumed to be well-integrated into rational decision-making models, it can be used to destabilise consultative processes, particularly when emotions are involved. Water policies are often seen as debates over technical and engineering issues, but can be highly controversial. Recycled water proposals in particular can create highly emotive conflicts. Through a case study regarding the rejection of recycled water proposals in southeast Queensland, Australia we explore the influence of science and emotions in contemporary water planning. We highlight the dangers inherent in promoting technical water planning issues at the expense of appropriate consideration of citizen concerns. Combining the science-policy interface and stakeholder engagement literatures, we advocate for collaborative decision-making processes which accommodate emotions and value judgements. A more collaborative stakeholder engagement model, founded on the principles of co-learning, has the potential to broaden the decision-making base and to promote better and more inclusive decision-making.