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 DE-Bay (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, the main focus of the paper concerns the coupling between the trunk space, the canopy and the above-canopy atmosphere. Therefore, relevant coherent structures were analyzed for different in- and above canopy layers, coupling between layers was classified according to already published procedures, and gradients and fluxes of meteorological quantities as well as concentrations of non-reactive and reactive trace compounds have been sorted along the coupling classes. Only in the case of a fully coupled system, it could be shown, that fluxes measured above the canopy are related to gradients between the canopy and the above-canopy atmosphere. Temporal changes of concentration differences between top of canopy and the forest floor, particularly those of reactive trace gases (NO, NO2, O3, and HONO) could only be interpreted on the basis of the coupling stage. Consequently, only concurrent and vertically resolved measurements of micrometeorological (turbulence) quantities and fluxes (gradients) of trace compounds will lead to a better understanding of the forest-atmosphere interaction.