The impact of biological bedforms on near-bed and subsurface flow: a laboratory evaluated numerical study of flow in the vicinity of pits and mounds

The complex surface topography of river substrates controls near‐bed hydraulics and drives the exchange of subsurface and surface flow. In rivers, the topographic structures that are studied are usually formed by the flow but, it is known that many animals also create biogenic bedforms, such as pits and mounds. Here, a Large‐Eddy Simulation (LES) model of flow over a pit and a mound is evaluated with flume experiments. The model includes actual bedform topography, and the topographic complexity of the surrounding bed surface. Subsurface grains are organized in a body‐centered cubic packing arrangement. Model evaluation showed strong agreement between experimental and modelling results for velocity (R2 > 0.8) and good agreement for Reynolds stresses (R2 > 0.7), which is comparable to other similar studies. Simulation of the pit shows that the length of the downwelling region is smaller than the upwelling region and that the velocity magnitude is higher in the downwelling region. Simulation of the mound reveals that the flow is forced into the bed upstream of the mound and re‐emerges near the top of the mound. The recirculation zone is limited at the leeside of the mound. With increasing Reynolds number, the depth of the upwelling region at the leeside of the mound increases. The analysis of shear stress indicates that sediments on the upstream edge of the pit and on the downstream face of the mound are relatively unstable. These results demonstrate the effect of biogenic structures on the near‐bed flow field, hyporheic exchange, and sediment stability.