The size and roughness characteristics of dunes in the Mississippi River are not predicted well by experimental and theoretical relations, even though intensive flow measurements were made in the study area. Although dunes increase in scale with increasing discharge of water and sediment, the development of multiple dune sizes and nonuniform flow obscure the relationship of dune geometry to synoptic hydraulic variables. Some nonuniformity is caused by the development of large bed undulations from kinematic waves that can deform into compound dunes, but most of it is related to flow convergence and divergence in pools and riffles, varying flow geometry with increasing stage, and reach-controlled relations between flow and energy loss. Even though changes of bedform size are not found to lag the flow changes because sand transport is large, a considerable volume of sediment is required to initiate and propagate the largest compound dunes. This means that they might be profiled in different stages of growth and have a varying effect on the flow during their evolution spatially and temporally.