The conflict between the conservation of biodiversity and recreation activities in the European landscape is intensifying. Managers of large nature areas are confronted with increasing numbers of visitors and decreasing biodiversity values. To accommodate the visitors while simultaneously protecting the biodiversity values they need to make changes in the landscape. Current legislation, a lack of knowledge on the recreation-biodiversity relationship, and the diverging point of view of stakeholders make it difficult to find consensual solutions. New approaches such as adaptive management and boundary management can help managers and stakeholders in the process of decision making. In these approaches the role of scientists has changed, as has the use of their tools. Using two research projects in Europe we explore how scientific tools are used in this new context. We argue that such tools (1) should be built on the interactions between recreation and biodiversity functions, (2) can be used interactively to encourage stakeholders to engage in a learning process, (3) allow local knowledge and data to be incorporated into them, and (4) generate output in the form of a map showing where the conflict areas and opportunities are located. These four key features will help managers to improve communication between themselves, stakeholders, and scientists, increase consensus between stakeholders on how the conflict should be perceived, explore solutions, and generate new knowledge. For future research we suggest investigating how adaptive management and boundary management can be used in a stepwise learning strategy and how uncertainties in the tools affect the learning process.