In ephemeral rivers, channel morphology represents a snapshot at the end of a succession of geomorphic changes caused by floods. In most cases, the channel shape and bedform migration during different phases of a flood hydrograph cannot be identified from field evidence. This paper analyses the timing of riverbed erosion and deposition of a gravel bed ephemeral river channel (Rambla de la Viuda, Spain) during consecutive and moderate- (March 2013) and low-magnitude (May 2013) discharge events, by applying a morphodynamic model (Delft3D) calibrated with pre- and post-event surveys by RTK-GPS points and mobile laser scanning. The study reach is mainly depositional and all bedload sediment supplied from adjacent upstream areas is trapped in the study segment forming gravel lobes. Therefore, estimates of total bedload sediment mass balance can be obtained from pre- and post-field survey for each flood event. The spatially varying grain size data and transport equations were the most important factors for model calibration, in addition to flow discharge. The channel acted as a braided channel during the lower flows of the two discharge events, but when bars were submerged in the high discharges of May 2013, the high fluid forces followed a meandering river planform. The model results showed that erosion and deposition were in total greater during the long-lasting receding phase than during the rising phase of the flood hydrographs. In the case of the moderate-magnitude discharge event, deposition and erosion peaks were predicted to occur at the beginning of the hydrograph, whereas deposition dominated throughout the event. Conversely, the low-magnitude discharge event only experienced the peak of channel changes after the discharge peak. Thus, both type of discharge events highlight the importance of receding phase for this type of gravel bed ephemeral river channel.