Characterising hydro-geomorphic character accurately is essential for understanding the processes whereby freshwater ecosystems maintain patterns of biodiversity and ecosystem processes. A key question is which temporal and spatial scales best represent the full diversity of habitat patches in riverine landscapes. Here, we characterise the hydrologic and geomorphic character of a large river-floodplain system (the Upper Mississippi River, USA) at multiple spatial and temporal scales. Seventeen variables are used to describe the hydro-geomorphic character of 99 backwaters and island lakes along 100km of the river. At the landscape scale (10s of kms), pool, position in pool and proximity to neighbouring patches were important in determining character. At the smaller patch scale (10s to 100s of m), the shape of entry to the patch, and water depth were distinguishing variables. There was clear variation too in relation to hydrologic character across temporal scales. At decadal time scales the nature of rises and falls separate patches, as does mean peak and duration of connection over long time periods. In contrast, the interplay of magnitude and duration of individual connection events produced unique patterns at inter-annual time scales. Importantly, different patterns are evident at different scales and picking up these patterns through a multi-scale approach provides a more complete view of the hydro-geomorphic character of the system. A clear understanding of how the physical template interacts with hydrology at different spatial and temporal scales provides a firm basis for investigating how biota interact with, and are influenced by, the system, with obvious implications for management.