Abstract <p>Turbulent flow around well-submerged, wall-mounted obstacles has been widely studied, but the effects of low relative submergence on the flow field remain less understood. While submergence effects have been examined in experiments, uncertainties persist in the three-dimensional flow characteristics around large obstacles, particularly regarding its role in shaping instream habitats and fish migration pathways. The complex flow generated by such obstacles plays a key ecological role in natural environments (e.g., rapids, tributaries), influencing sediment transport, refuge zones, and turbulence structures that affect aquatic species. However, volumetric time-resolved measurements covering the upstream, side, and wake regions remain scarce. To examine the impact of submergence on the flow field, this study conducts laboratory flume experiments employing 3D Lagrangian particle tracking to assess two submergence levels around a wall-mounted cube. The response of key mean flow parameters, including streamwise and vertical velocities, as well as the production of turbulent kinetic energy, was examined, and time-resolved flow fields were analyzed using power spectra and proper orthogonal decomposition. Major vortical structures around the cube, namely horseshoe and arch vortices, are identified and analyzed. The study reveals that variations in relative submergence and shallow flow conditions strongly influence the flow field, with lower relative submergence being associated with increased flow complexity. These variations affect flow structures that govern habitat formation and fish migration. The insights gained contribute to a better understanding of flow around large obstacles, supporting ecological engineering and habitat restoration efforts in shallow waterways.</p> Graphic Abstract