Microclimate was investigated within a heterogeneous spruce forest in Northern Bavaria, Germany, at theWaldstein-Weidenbrunnen site, especially during the EGER project in 2007, 2008 and 2011. Besides standard tower measurements, two innovative measuring techniques were used to investigate horizontal and vertical gradients. A particular focus was paid to advection within the homogeneous part and its effect on net ecosystem exchange, as well as gradients near a forest edge, measured by a mobile measuring system. The forest canopy shields the below-canopy trunk space and therefore huge gradients are prevalent. However, vertical exchange is PAI-dependent and thus small gaps in the canopy (‘sunny spots’) can facilitate vertical exchange by coherent structures and alter the CO2 concentration within the trunk space. The coupling of different canopy layers also plays an important role in altering trunk space conditions. Decoupling leads to an enrichment of CO2 close to the ground with large katabatic drainage, and coupling leads to depletion. Furthermore, the investigations showed that horizontal and vertical advection contributes significantly to the net ecosystem exchange at the Waldstein-Weidenbrunnen site, especially during nighttime and transition periods. The investigations in 2011 showed that clearings, with their forest edges, play a key role in vertical exchange in heterogeneous forests. Roughness changes and thermal differences between forests and clearings facilitate downdrafts (during night) and updrafts (during day). This leads to the highest variations in turbulent influenced quantities, like temperature, humidity and trace gas concentrations directly at the forest edge, for example. Additionally, the formation of a secondary circulation system is possible above the clearing during midday, with effects on horizontal gradients.