The spatial variations of water and energy budgets are highly influenced by the heterogeneity of land-surface characteristics. We investigate the spatiotemporal variability and dependence structure patterns of water and energy fluxes along an elevation gradient. Our analysis is based on the application of the GEOtop model and empirical Copulas. It is performed for the Rott (∼55 km2) and Upper-Ammer (∼300 km2) catchments in the TERrestrial ENvironmental Observatories prealpine region over two recent summer episodes, as a test case. We found that GEOtop is capable of quantifying the spatiotemporal variability of the water and energy budgets with consideration for the elevation-gradient effect of this heterogeneous landscape, which is confirmed by the linear statistical metrics. Furthermore, the empirical Copula-based function reveals that the dependence structures between the measured and simulated hydrometeorological variables are similar either at upper or lower density maxima. This suggests a reasonable performance of the model, as the interaction of variables is described properly; however, the model shows poorer performance in the middle ranks of the data. It is concluded that the presented Copula-based model performance analysis is a valuable complement to traditional global performance model analyses.