The potential ecological effects of cockle fisheries and gas exploitation in the Dutch Wadden Sea and their implications for policy and management have been the topic of vigorous societal debates. Ecological science has played crucial but controversial roles in these debates. Several social science studies have been dedicated to analysing these roles and making recommendations for the improvement of science–policy interactions. In reviewing these studies, this article aims to draw lessons for (ecological) scientists and policy makers on how to understand and guide the interactions of science and policy in Wadden Sea management. Studies addressing science–policy interactions in the Dutch Wadden Sea can be grouped into three main perspectives, emphasizing the social and economic dynamics of resource management, the role of nature views and discourses in controversies, and the influence of science dynamics in policy and management debates. The review demonstrates that ecological knowledge and ecological scientists have played important roles in the controversies on cockle fisheries and gas exploitation. However, scientific knowledge was not always the most important factor in the decision-making process, and scientific insights were not always used as expected by the scientists. How scientific knowledge is used and interpreted by stakeholders was dependent on their interests, their nature views and on the dominant policy discourses. Ecological knowledge and scientists themselves became part of the policy debates, e.g. in discussions on uncertainty and reliability. The position of scientists in policy debates was strongly influenced by the policy setting and by changes in this setting, e.g. by the operation of mediators or by new interpretations of legal rules. A lesson to be drawn for scientists is that they should reflect on the sort of position – e.g. independent outsider, or engaged stakeholder – they take in a debate. They should also be aware that this position cannot be chosen at will: it is strongly influenced by the policy context. For government and other stakeholders, an important lesson is that by shaping adequate policy settings they can contribute to more productive and effective interactions with science and scientists.