To investigate the energy, matter and reactive and non-reactive trace gas exchange between the atmosphere and a spruce forest in the German mountain region, two intensive measuring periods were conducted at the FLUXNET site Waldstein-Weidenbrunnen in September/October 2007 and June/July 2008. They were part of the project “ExchanGE processes in mountainous Regions” (EGER). Beyond a brief description of the experiment and links to the already published results of both experiments, the main focus of the paper is the problem of the coupling of the trunk space, the canopy and the atmosphere. Therefore, the relevant coherent structures were analyzed in different canopy levels and an already published coupling classification was applied to gradients and fluxes. It could be shown that fluxes above the canopy are only related to the gradient between the canopy and the atmosphere in the case of a fully coupled system. Changes in the concentration of especially reactive trace gases (NO-NO₂-O₃ and HONO) could only be interpreted together with the coupling stage. Finally it was pointed out that the combination of air chemical measurements with micrometeorological turbulence measurements is urgently needed to understand the biosphere-atmosphere interaction.