Flood water in an alluvial channel (or river) conveys suspended sediments from upstream to downstream, and entrains bed materials along with flood currents. Morphological changes on channel/river bed trend to reduce the conveyance capability of channel, and then to affect water stages and discharges. It is therefore necessary to quantify the influence of sediment transport on variations of water stages for the purpose of best flood water management in alluvial rivers. This paper presents a simulation-based optimization model to systematically investigate optimal control of flood stages for various geometries and sediment properties in alluvial channels. This integrated system consists of a well-established one-dimensional river flow model and a non-uniform/non-equilibrium sediment transport model, as well as an adjoint model for determining the sensitivity of objective function. Flood control is demonstrated by operating a single floodgate and multiple gates to withdraw flood waters from alluvial channel. The optimal withdrawal hydrographs for scheduling the floodgate opening operations are obtained under the constraints of objective water stages applied to target reaches. It is found that the influence of morphological changes on flood control becomes significant under certain hydrological and morphological conditions, and varies with the installation of control structures. This preliminary study shows that this simulation-based optimization model is effective to facilitate best management of flood and sediment transport and design of control structures in alluvial channels/rivers. (C) 2011 Elsevier B.V. All rights reserved.