Traditional top-down and technocratic approaches seem to be insufficient to tackle the many conflicts related to the sustainable use of natural resources. At the same time, reductionist and mono-disciplinary approaches lack the capacity to capture the complex interactions within evolving socio-ecological systems. Coastal zone management is an area that provides a clear example of such difficulties. In this paper we explore the scope of a participatory integrated assessment process, known as Social Multi-Criteria Evaluation (SMCE), in the context of Integrated Coastal Zone Management (ICZM). Through a two-year collaborative research process, between an interdisciplinary group of researchers and a diverse group of stakeholders in the Urdaibai Estuary (a Biosphere Reserve in the Basque Country, Northern Spain), we show that improving the integration of diverse expertise and values can lead, through a mutual learning process, to the definition of relevant policy options and sound decisions in the face of complexity, value conflict and unavoidable uncertainty. © 2010 Elsevier Ltd.