Habitats or environmental factors that convey spatial and temporal resistance and/or resilience to biotic communities that have been impacted by biophysical disturbances may be called refugia. Most refugia in rivers are characterized by extensive coupling of the main channel with adjacent streamside forests, floodplain features, and groundwater. These habitats operate at different spatial scales, from localized particles, to channel units such as pools and riffles, to reaches and longer sections, and at the basin level. A spatial hierarchy of different physical components of a drainage network is proposed to provide a context for different refugia. Examples of refugia operating at different spatial scales, such as pools, large woody debris, floodplains, below dams, and catchment basins are discussed. We hope that the geomorphic context proposed for examining refugia habitats will assist in the conservation of pristine areas and attributes of river systems and also allow a better understanding of rehabilitation needs in rivers that have been extensively altered.