Monitoring coastal seabed in very shallow waters (0–5 m) is a challenging methodological issue, even though such data is of major importance to many scientific and technical communities. Over the years, Structure-from-Motion (SfM) photogrammetry has emerged as a flexible and inexpensive method able to provide both a 3D model and high-resolution imagery of the seabed (~cm level). In this study, we propose a low-cost (about USD 1500), adaptable, lightweight and easily dismantled system called POSEIDON (for Platform Operating in Shallow-water Environment for Imaging and 3D reconstructiON). This prototype combines a floating support (typically a bodyboard), two imagery sensors (here, GoPro® cameras) and an accurate positioning system using Real Time Kinematic GNSS. Validation of this method was deployed in a macrotidal zone, comparing on the foreshore the point cloud provided by POSEIDON “SfM bathymetry” and by classical terrestrial SfM survey. Mean deviation was 5.2 cm and standard deviation was 4.6 cm. Such high-resolution SfM bathymetric surveys have a great potential for a wide range of applications: micro-bathymetry, hydrodynamics (bottom roughness), benthic habitats, ecological inventories, archaeology, etc.