Water exchange between streams and hyporheic zones is highly dynamic, and its temporal variation is related to the hydrologic fluctuations of stream discharge and groundwater levels. Unfortunately, predictions of temporal patterns of exchange are difficult due to the many hydrodynamic and morphodynamic processes that are involved and also to their complex nonlinear interactions. Examples of these processes include the evolution of streambed morphology in response to changing streamflow as well as the feedback on surface flow induced by drag resistance due to evolving bed forms. In this work, we have employed a stochastic method to analyze the temporal dynamics of bed form-driven hyporheic exchange in a stream characterized by subcritical flow and daily discharge variations. The method is an extension of previous studies that includes current-induced alterations of bedform size and celerity and their effect on water exchange. The modeling results show that during high flows, stream water penetrates deeper and for longer times in the sediments. At the same time, the predicted rate of water exchange per unit streambed area decreases because the streambed area occupied by each bed form increases faster than the volumetric rate of stream water exchange induced by the same bed form. This reduction can be compensated by the increase in wetted area with discharge, which may provide additional streambed area for water exchange. One the main finding of the study is that the time-averaged values of exchange flux and depths are quite similar to those modeled for a steady mean discharge, while residence times are somewhat lower. Predicted temporal variations of exchange depths and times around their time-averaged values are moderate compared to steady state values.