Mobile boundaries are a frequent feature of environmental flows. Common examples of mobile boundaries are the changing bed morphology due to sediment transport, vegetation boundaries, or mobile elements such as schools of fish and patches of mussels. Boundary mobility introduces temporal and spatial heterogeneities that complicate the experimental or numerical investigation of such flows, due to the related difficulties in measurement or simulation and data interpretation. The time and space averaging framework, known as the double-averaging methodology, was formulated to facilitate the study of such cases. In this paper, the double-averaging methodology is applied to the analysis of a data set obtained by direct numerical simulation (DNS). The DNS model represents open-channel flow over a granular bed with small relative submergence. A plane layer of fixed particles, with overlaying mobile particles, form the bottom domain boundary. The objective of this study is to identify the underlying physical mechanisms by performing a scale analysis of the relevant terms included in equations that describe the balance of the kinetic energy. It is anticipated that this investigation will assist in the analysis of experimental data sets and in the development of improved predictive models. The potential use of this approach in flow-biota interaction studies is also discussed with examples.