Context: Describing the hydrogeomorphic character of rivers in a holistic way is essential to understanding the processes whereby freshwater ecosystems maintain patterns of biodiversity and ecosystem processes. A key question in carrying out this characterisation is the temporal and spatial scales which best represent differences and similarities between habitats. Objectives: The purpose of this study is to describe the hydrological and geomorphological character of a large river-floodplain system (the Upper Mississippi River, USA) at multiple spatial and temporal scales in order to holistically determine the physical template influencing the riverine ecosystem. Methods: Seventeen variables are used to describe the hydrogeomorphic character of 99 backwaters and floodplain lakes along a 100 km reach of the river. Results: At the landscape scale (10 s of km), position in the landscape and proximity to neighbouring habitats contributed most to variability in hydrogeomorphic character. At the smaller patch scale (10–100 s of m), the shape of entry to the patch and water depth were distinguishing variables. In relation to temporal variables, habitats are distinguished by decadal scale variables describing the historic nature of the rise and fall of connection events, and mean peak and duration of connection over long periods. In contrast, the interplay of magnitude and duration of individual connection events produced unique patterns at the short-term temporal scale (intra-annual). Analysis of all variables across all scales showed that no variable from one scale of observation was dominant, rather variables from multiple scales are contributing to hydrogeomorphic character to varying degrees. Conclusions: This work demonstrates how an interdisciplinary, multi-scale approach is critical in detecting unique patterns in hydrogeomorphic character across different spatial and temporal scales. This approach enables a holistic view of spatio-temporal heterogeneity of a system and provides a firm basis for investigating how the physical template influences and helps to maintain patterns of biodiversity and ecosystem processes in complex and dynamics systems.