Abstract. For an assessment of the role of soil and vegetation in the climate system, a further understanding of the flux components of H2O and CO2 (e.g., transpiration, soil respiration) and their interaction with physical conditions and physiological functioning of plants and ecosystems is necessary. To obtain magnitudes of these flux components, we applied the source partitioning approaches after Scanlon and Kustas (2010; SK10) and after Thomas et al. (2008; TH08) to high frequency eddy covariance measurements of twelve study sites including various ecosystems (croplands, grasslands, and forests) in a number of countries. Both partitioning methods are based on higher-order statistics of the H2O and CO2 fluctuations, but proceed differently to estimate transpiration, evaporation, net primary production, and soil respiration. We compared and evaluated the partitioning results obtained with SK10 and TH08 including slight modifications of both approaches. Further, we analyzed the interrelations between turbulence characteristics, site characteristics (such as plant cover type, canopy height, canopy density and measurement height), and performance of the partitioning methods. We could identify characteristics of a data set as prerequisite for a sufficient performance of the partitioning methods. SK10 had the tendency to overestimate and TH08 to underestimate soil flux components. For both methods, the partitioning of CO2 fluxes was more irregular than of H2O fluxes. Results derived with SK10 showed relatively large dependencies on estimated water use efficiency (WUE) at leaf-level, which is needed as an input. Measurements of outgoing longwave radiation used for the estimation of foliage temperature and WUE could slightly increase the quality of the partitioning results. A modification of the TH08 approach, by applying a cluster analysis for the conditional sampling of respiration/evaporation events, performed satisfactorily, but did not result in significant advantages compared to the other method versions (developed by Thomas et al., 2008). The performance of each partitioning approach was dependent on meteorological conditions, plant development, canopy height, canopy density, and measurement height. Foremost, the performance of SK10 correlated negatively with the ratio between measurement and canopy height. The performance of TH08 was more dependent on canopy height and leaf area index. It was found, that all site characteristics which increase dissimilarities between scalars enhance partitioning performance for SK10 and TH08.