Abstract. In this study we present a combined soil/canopy chamber system that allows the investigation of carbon flow through the atmosphere-plant-soil system via a ¹³CO₂ canopy labelling approach – especially when using short vegetation such as tree saplings. The developed chamber system clearly separates soil and canopy compartment in order to (a) prevent physical diffusion of ¹³C tracer into the soil chamber during a ¹³CO₂ canopy pulse labelling (b) study stable isotope processes in soil and canopy individually and independently. In combination with novel laser spectrometry, measuring CO₂ (Aerodyne Research Inc.) and H₂O (Los Gatos Research Inc.) isotopologue mixing ratios at a rate of 1 Hz, we were able to trace the label transport from leaves to roots in small beech saplings (Fagus sylvatica L.) without interference due to contamination of the soil matrix and/or canopy re-labelling via tracer returning from soil respiration. A very tight coupling between above- (photosynthesis) and belowground (soil respiration) processes was found, where newly assimilated carbon fixed from the ¹³CO₂ atmosphere re-appeared in soil respiration 2 h after it has been photosynthetically fixed. We were able to demonstrate that leaf metabolism acts on substrate for soil respiration on a diurnal timescale, with input of fresh photosynthates during daytime and starch re-mobilisation during nighttime. Long-term fluctuations in the δ¹³C of soil respiration, as observed under reduced water availability, could not be described by any biological or instrumental mechanism, as they did occur in an atypical ca. 15 hourly rhythm – potential mechanisms driving these fluctuations are hypothesized.