Based on a Dutch case study on shellfish fishery policy making and a literature review, we expand existing guidelines for coastal zone management. We deduce constraints for handling societally contested and scientifically complex environmental issues. Our additions focus on problem structuring and handling of scientific uncertainties. Both are means to increase consensus about beliefs, ambitions, and directions for solutions. Before policy making can take place, complex environmental issues need to become more structured by reducing either scientific uncertainty or societal dissent: the "pacification strategy" and the "facilitation strategy," respectively. We show that the use of a pacification strategy, in which science is expected to pacify stakeholders, is not an answer, as uncertainties are likely to remain high due to a different pacing of scientific progress and policy-making demands. Instead, we propose a facilitation strategy in which stakeholders formulate shared ambitions and directions for solutions at an early stage, and ecological scientists extend their participation in the process by scientifically assessing policy alternatives. With an eye to giving ecological science a significant role in policy making and management, we present an improved set of guidelines, incorporating the facilitation strategy by focusing on balancing economic and ecological interests and shared policy formulation by scientific inquiry instead of political opportunity.