This work presents recent advances on morphodynamic modeling of bed forms under unsteady discharge. This paper includes further development of a morphodynamic model proposed earlier by Giri and Shimizu (2006a). This model reproduces the temporal development of river dunes and accurately replicates the physical properties associated with bed form evolution. Model results appear to provide accurate predictions of bed form geometry and form drag over bed forms for arbitrary steady flows. However, accurate predictions of temporal changes of form drag are key to the prediction of stage-discharge relation during flood events. Herein, the model capability is extended to replicate the dune–flat bed transition, and in turn, the variation of form drag produced by the temporal growth or decay of bed forms under unsteady flow conditions. Some numerical experiments are performed to analyze hysteresis of the stage-discharge relationship caused by the transition between dune and flat bed regimes during rising and falling stages of varying flows. The numerical model successfully simulates dune–flat bed transition and the associated hysteresis of the stage-discharge relationship; this is in good agreement with physical observations but has been treated in the past only using empirical methods. A hypothetical relationship for a sediment parameter (the mean step length) is proposed to a first level of approximation that enables reproduction of the dune–flat bed transition. The proposed numerical model demonstrates its ability to address an important practical problem associated with bed form evolution and flow resistance in varying flows.