According to Dooge (1986) intermediate-scale catchments are systems of organized complexity, being too organized and yet too small to be characterized on a statistical/conceptual basis, but too large and too heterogeneous to be characterized in a deterministic manner. A key requirement for building structurally adequate models precisely for this intermediate scale is a better understanding of how different forms of spatial organization affect storage and release of water and energy. Here, we propose that a combination of the concept of hydrological response units (HRUs) and thermodynamics offers several helpful and partly novel perspectives for gaining this improved understanding. Our key idea is to define functional similarity based on similarity of the terrestrial controls of gradients and resistance terms controlling the land surface energy balance, rainfall runoff transformation, and groundwater storage and release. This might imply that functional similarity with respect to these specific forms of water release emerges at different scales, namely the small field scale, the hillslope, and the catchment scale. We thus propose three different types of "functional units" - specialized HRUs, so to speak - which behave similarly with respect to one specific form of water release and with a characteristic extent equal to one of those three scale levels. We furthermore discuss an experimental strategy based on exemplary learning and replicate experiments to identify and delineate these functional units, and as a promising strategy for characterizing the interplay and organization of water and energy fluxes across scales. We believe the thermodynamic perspective to be well suited to unmask equifinality as inherent in the equations governing water, momentum, and energy fluxes: this is because several combinations of gradients and resistance terms yield the same mass or energy flux and the terrestrial controls of gradients and resistance terms are largely independent. We propose that structurally adequate models at this scale should consequently disentangle driving gradients and resistance terms, because this optionally allows equifinality to be partly reduced by including available observations, e.g., on driving gradients. Most importantly, the thermodynamic perspective yields an energy-centered perspective on rainfall-runoff transformation and evapotranspiration, including fundamental limits for energy fluxes associated with these processes. This might additionally reduce equifinality and opens up opportunities for testing thermodynamic optimality principles within independent predictions of rainfall-runoff or land surface energy exchange. This is pivotal to finding out whether or not spatial organization in catchments is in accordance with a fundamental organizing principle.