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Abstract Quantification of velocity and pressure fields over streambeds is important for predicting sediment mobility, benthic and hyporheic habitat qualities, and hyporheic exchange. Here, we report the first experimental investigation of reconstructed water surface elevations and three‐dimensional time‐averaged velocity and pressure fields quantified with non‐invasive image techniques for a three‐dimensional free surface flow around a barely submerged vertical cylinder over a plane bed of coarse granular sediment in a full‐scale flume experiment. Stereo particle image velocimetry coupled with a refractive index‐matched fluid measured velocity data at multiple closely‐spaced parallel and aligned planes. The time‐averaged pressure field was reconstructed using the Rotating Parallel Ray Omni‐Directional integration method to integrate the pressure gradient terms obtained by the balance of all the Reynolds‐Averaged Navier‐Stokes equation terms, which were evaluated with stereo particle image velocimetry. The detailed pressure field allows deriving the water surface profile deformed by the cylinder and hyporheic flows induced by the cylinder.