Spatial and temporal environmental heterogeneity in lotic ecosystems can be quantitatively described and identified with characteristic levels of ecological organization. The long-term pattern of physicochemical variability in conjunction with the complexity and stability of the substratum establishes a physical habitat template that theoretically influences which combinations of behavioral, physiological and life history characteristics constitute appropriate “ecological strategies” for persistence in the habitat. The combination of strategies employed will constrain ecological response to and recovery from disturbance. Physical habitat templates and associated ecological attributes differ geographically because of biogeoclimatic processes that constrain lotic habitat structure and stability and that influence physicochemical variability and disturbance patterns (frequency, magnitude, and predictability). Theoretical considerations and empirical studies suggest that recovery from natural and anthropogenic disturbance also will vary among lotic systems, depending on historical temporal variability regime, degree of habitat heterogeneity, and spatial scale of the perturbation. Characterization of physical habitat templates and associated ecological dynamics along gradients of natural disturbance would provide a geographic framework for predicting recovery from anthropogenic disturbance for individual streams. Description of lotic environmental templates at the appropriate spatial and temporal scale is therefore desirable to test theoretical expectations of biotic recovery rate from disturbance and to guide selection of appropriate reference study sites for monitoring impacts of anthropogenic disturbance. Historical streamflow data, coupled with stream-specific thermal and substratum-geomorphologic characteristics, are suggested as minimum elements needed to characterize physical templates of lotic systems.