Detailed field measurements and simulations of three-dimensional flow structure were used to develop a conceptual model to explain the sustainability of self-formed pool-riffle sequences in gravel-bed rivers. The analysis was conducted at the Red River Wildlife Management Area in Idaho, USA, and enabled characterization of the flow structure through two consecutive pool-riffle sequences, including: identification of jet concentration and dissipation zones, and the development of local turbulence features (i.e. vertical and horizontal eddies) under different flow conditions. Three-dimensional hydraulic simulations were used to evaluate how the flow structure varies across a range of flow conditions and with different degrees of sediment aggradation within the upstream pool. The analysis demonstrated a significant influence of the residual pool depth on the flow structure, with reduced residual depth causing a shift in the orientation of the jet and a reduction in the influence of vertical eddies and the size and intensity of horizontal eddies. The proposed conceptual model seeks to explain the sustainability of pools in terms of the flow structure in pool-riffle morphology and how this flow structure will change as a result of altered external forcing, such as upstream sediment delivery or changes in bank stability. Copyright © 2010 John Wiley & Sons, Ltd.