In regulated rivers and small streams, the presence of large roughness elements like boulders and concrete structures significantly impacts the local flow field and creates complex hydraulic conditions important for aquatic habitats. This study focuses on investigating and analyzing the complex three-dimensional flow field around an idealized stone (represented as a hemisphere) to understand how the flow field changes for different relative depths i.e. water depth relative to boulder height, and flow rates. Time-resolved 3D Particle Tracking Velocimetry was employed in laboratory experiments conducted in an open-channel flume, to mimic varying river conditions and their impact on flow characteristics. Results reveal that the relative depth significantly influences the flow structure behind the hemisphere, impacting recirculation zones and wake characteristics. The flow field behind the hemisphere was found to be more sensitive to changes in relative depth than bulk velocity. The study also highlights the larger regions of lower streamwise velocity that occurred downstream of the hemisphere caused by the lower submergences combined with a higher magnitude of the downward vertical velocity. Furthermore, this study demonstrates the capability of the measurement technique and the time-resolved 3D Particle Tracking Velocimetry system used to effectively capture the complex flow dynamics around the boulder. This approach allowed for detailed visualization and quantification of flow parameters such as streamwise and vertical velocities within the wake region, which are important factors for aquatic habitats. Understanding the underlying flow dynamics around an idealized stone at low relative depths could yield insights into ecohydraulic engineering and ecological restoration in shallow streams. This can contribute to advancing our understanding of riverine flow dynamics and their ecological implications.