Local widening in a channelized river is a common practice in restoration projects. The lateral embayments built for this purpose in the river banks are partially filled up by fine sediments. This allows the formation of aquatic habitats with hydraulic and morphologic diversity. However, the design of these lateral cavities may be compromised by the fluctuations in the water discharge. To address this problem, systematic experimental investigations have been carried out with five different fluctuating hydrograph scenarios. Water depth, sediment concentration and area covered by the settled sediments are analysed in each experiment. The process of sedimentation in the lateral embayments proved to be, in general, resilient to flow fluctuations. However, there were several differences observed during the high flow phase fluctuation phase depending on the geometric configuration of the embayments and the applied hydrograph: (i) a higher peak in discharge means that more sediments are resuspended and a complete remobilization of the in-cavity sediment deposits is possible. (ii) Long and short cavities are more resilient to high flow events than cavities with an intermediate length.