Obtaining a better knowledge of how flow variability affects lotic biota is of considerable importance to stream and river management. We contend that processes at different hierarchical levels of organization in lotic ecosystems are sensitive to variation in flow at related hierarchical temporal scales. Ecosystem disturbance caused by large-scale events (i.e. infrequent, but high magnitude flow events with a recurrence interval of years to many days) tend to determine high-level characteristics of ecosystem structure (e.g. determining species pools, periphyton versus macrophyte dominance) and function (e.g. balance between auto- and heterotrophy). The high-level ecosystem characteristics then set the stage for processes that are influenced by flow variation that occurs at smaller temporal scale (i.e. minutes to milliseconds) such as colonization, biotic interactions and mass transfer enhancement of production. We contend that large-scale temporal events predominantly affect lotic ecosystems through physical drag processes (‘drag-disturbance’), whereas small-scale flow variations affect ecosystems through mass-transfer processes (including invertebrate and fish food-uptake). Drag-disturbance and mass-transfer related processes mark the opposite ends of a continuum of flow variability controlled processes, with moderate temporal scale flow variability events affecting ecosystems through both drag-disturbance and mass-transfer processes in similar proportions. Flow variability, and associated effects on ecosystems, across these scales is discussed with reference to New Zealand rivers. We suggest that these concepts can be integrated across the full range of temporal scales based on a spectrum of velocity variations. This may provide a unifying conceptual model for how the structure and functioning of lotic ecosystems are linked to flow variability. Copyright © 2005 John Wiley & Sons, Ltd.