Using selected examples of recent research, this paper illustrates the role of abiotic components within running-water ecosystems. The important role of temperature is acknowledged but the paper focuses on another key driver: physical stability, defined in relation to hydrological (frequency, duration and timing of inundation) and substratum parameters (channel dynamics, bedform and sediment size). The importance of this driver is illustrated by reference to four spatial scales. At the scale of the bedform, surface-water and groundwater interactions play an important role not least in driving energy exchanges and determining the temperature dynamics within the ecologically important surface layer of the bed sediments. At the reach scale, bedform development, channel form dynamics, and associated changing hydraulic conditions determine both benthic and riparian community patterns. At the catchment scale, new research has shown that the processes responsible for the formation of islands and divided channels play important roles in the functioning of fluvial hydrosystems. Finally, at the regional scale, the flow regime modified by the geomorphological history of the river over at least the past 16 000 years explains ecological patterns. The integration of hydro-geomorphological knowledge from all four scales of analysis is shown to be fundamental for understanding the ecological characteristics of running waters and for managing ecological integrity.