Currently, many ecosystems are increasingly affected by human activities, such as disturbance, overfishing, fragmentation and pollution. However, these activities have not only negative effects on ecosystems, societal systems are also affected negatively, as appears from e.g. decreasing fish caught and climate change. This demonstrates the mutual dependency of natural and societal systems. Because of the increasing interaction between both systems we may even speak of hybrid systems, especially when such ecosystems are closely located to human systems. This is true for many coastal ecosystems around the world. From this point of view conservation and restoration sciences can be seen as attempts to understand the interactions between both systems in order to contribute to the conservation or natural enhancement of such ecosystems. Successful conservation and restoration depend on well matched conservation measures with respect to ecological structures and processes. Several authors have pointed at the problem of scale-discordance, i.e. the mismatch between the temporal and spatial scales of ecological analysis on the one hand and management and governance measurements on the other hand. Especially coastal ecosystems, which often have a long history of human utilization and thus of tradition embedded management systems may suffer from such a mismatch. We have analyzed the appearance of scale discordance with respect to human coastal fishery activities in the Dutch Wadden Sea, a widely recognized natural area that is located at the rim of one the most densely populated areas of the European continent. It appears that assessing and managing complex and multi-scaled environmental and ecological systems require an integrated multi-level and multi-scale approach. Since most expertise is related to a particular scale and often to a particular level within a scale, there is a strong need to integrate and coordinate the multiplicity of different expertises involved.