Partitioning net ecosystem CO2 fluxes measured by the eddy covariance technique into their components assimilation and respiration is crucial for predicting future responses and feedbacks of ecosystems to a changing climate. On the basis of an isotopic approach with 13C, we partitioned the daytime net CO2 fluxes of a deciduous forest in central Germany into assimilation and respiration fluxes over a period of 3 weeks. This is the first attempt so far to quantify component fluxes with stable isotopes over the period of 3 weeks, enabling us to investigate the impact of environmental factors on the partitioned fluxes. Large variability in environmental conditions during the 3-week measurement campaign led to strong changes in isotopic disequilibrium between assimilation and respiration, ranging from 1 to 5?. Although this approach is still associated with large uncertainty, we found reasonable patterns in ecosystem respiration and assimilation, and a significant correlation of daytime respiration with soil temperature (R2 = 0.48). The ratio of respiration to assimilation was highly variable on a day-to-day basis, ranging from 10% to more than 25%. This ratio was mainly controlled by soil temperature (R2 = 0.61), indicating a strong sensitivity of ecosystem carbon dynamics to temperature changes and higher carbon uptake efficiency during cooler days.