Policy-makers and scientists often expect that controversies in public policy can be solved by gathering more knowledge, even though this linear model of expertise is widely criticised in social studies of science. To shed more light on this expectation, the role of scientific uncertainties in controversies on mussel fishery in the Dutch Wadden Sea (1990–2016) is investigated. The analysis shows that mussel fishery regulation decisions were primarily based on government authority, not on scientific knowledge. Expectations of policy-makers and scientists on conflict resolution by more research were not met, because the knowledge debate was politicised over ambiguous knowledge claims. The controversy was depoliticised by a political covenant between the conflicting parties. The case study confirms that science-based knowledge fails to guide policy-making as expected in the linear model, and demonstrates how science plays important strategic, procedural and instrumental roles in structuring interactions between stakeholders in nature protection conflicts.