Policies and management for the Wadden Sea, like for so many other nature areas, have to find a balance between important natural values on the one hand and economic functions on the other hand. Scientific experts play an important role in these processes. In the case of the Wadden Sea, scientific experts have been involved in the development of trilateral ecological targets for the Wadden Sea as well as in the implementation of these targets in the Netherlands as took place in the controversial decision making processes regarding cockle fisheries and gas mining. Drawing on concepts and insights from policy analysis and science and technology studies, this article analyses the different roles scientific experts play in these policy processes. We show how the role of science shifts from an accommodating role in policy development to a role as advocacy in controversial policy implementation processes. The article concludes with some implications for organising effective science-policy interactions in the field of nature conservation. © 2007 Elsevier Ltd. All rights reserved.