Abstract Hydrodynamic and morphodynamic forces interacting across the sediment‐water interface control the biogeochemistry in the hyporheic zone. When investigating the redox zonation within streambeds, dissolved oxygen (O 2 ) is considered a key solute to the understanding of river ecosystems. However, no field studies have measured the spatiotemporal O 2 distribution linked to bedform celerity induced by changes in stream water velocity. Therefore, we developed and tested an innovative in situ setup in the River Erpe, Germany. The setup combines a planar O 2 optode and O 2 flow‐through cells for eight sediment depths to capture the variability in O 2 dynamics, and a laser scanner to capture bedform morphodynamics, which was used to calculate bedform celerity. The setup was tested under different stream water velocities between 0.1 and 0.5 m/s. We found that O 2 patterns in the streambed depend on stream water velocity. At low velocities, bedforms were stationary and a stable redox zonation with limited O 2 penetration in the streambed (up to 4 cm) was observed. As we increased the velocity up to 0.3 m/s, the spatiotemporal variability of O 2 distribution across the bedform increased, with anoxic patches moving along the migrating bedforms. At the highest velocity tested (0.5 m/s), the sediment bed was constantly oxygenated with deeper O 2 penetration as compared to slower velocities. The present study provides proof of concept for in situ O 2 measurements in small rivers, which helps to refine laboratory and mesocosm experiments, improve the knowledge of the processes involved in natural environments, and develop more sustainable river management strategies.