Intertidal mudflats play a critical role in estuarine exchange, connecting marine and continental supplies of nutrients and sediments. However, their complex morphodynamics, associated with a wide range of physical and biological processes, are still poorly understood and require further field investigation. In addition, mudflats are challenging areas for Structure-from-Motion (SfM) photogrammetric surveys. Indeed, the mudflats generally hold back residual tidal water, which can make stereo restitution particularly difficult because of poor correlations or sun-glint effects. This study aims to show the potential of light UAVs (Unmanned Aerial Vehicles) for monitoring sedimentary hydrodynamics at different spatial scales in a silty estuary. For each UAV mission an orthophotograph and a Digital Elevation Model (DEM) are computed. From repeated surveys the diachronic evolution of the area can be observed via DEM differencing. Considering the ground texture in such a context, the stereo restitution process is made possible because of the high spatial resolution of the UAV photographs. Providing a synoptic view as well as high spatial resolution (less than 4 cm), the UAV dataset enables multi-scale approaches from the study of large areas to the morphodynamics of smaller-scale sedimentary structures and the morphodynamics impact of plant ground cover.