Competing claims on natural resources become increasingly acute, with the poor being most vulnerable to adverse outcomes of such competition. A major challenge for science and policy is to progress from facilitating univocal use to guiding stakeholders in dealing with potentially conflicting uses of natural resources. The development of novel, more equitable, management options that reduce rural poverty is key to achieving sustainable use of natural resources and the resolution of conflicts over them. Here, we describe an interdisciplinary and interactive approach for: (i) the understanding of competing claims and stakeholder objectives; (ii) the identification of alternative resource use options, and (iii) the scientific support to negotiation processes between stakeholders. Central to the outlined approach is a shifted perspective on the role of scientific knowledge in society. Understanding scientific knowledge as entering societal arenas and as fundamentally negotiated, the role of the scientist becomes a more modest one, a contributor to ongoing negotiation processes among stakeholders. Scientists can, therefore, not merely describe and explain resource-use dynamics and competing claims, but in doing so, they should actively contribute to negotiation processes between stakeholders operating at different scales (local, national, regional, and global). Together with stakeholders, they explore alternatives that can contribute to more sustainable and equitable use of natural resources and, where possible, design new technical options and institutional arrangements.