Factors such as flow and sediment characteristics affecting the spur dike’s local depth of erosion have yielded considerable research results, but there is little discussion of the geometry of the spur dike’s local scour holes. This study focuses on the spatial characteristics of the geometry of local scour holes in straight-wall spur dikes. The discussion shows that the spur dike arrangement clearly changes the plane geometry of the scour hole. The maximum scour depth has a power function relationship with the area of the scour hole and the scour hole-volume. Moreover, the ratio of the product of the maximum scour depth and the plane area of the scour hole to the scour hole-volume is a fixed constant. The average slope of upstream of the scour hole and along the axis direction of the spur dike is slightly larger than the angle of repose of the sediment, the slope distribution of the scour holes profiles presents an inverted “U” type, and its profile morphology and slope distribution have geometric similarity. This distribution also reflected that, the interaction between the downward flow and the horseshoe vortex inside the scour hole leads to the formation of a cusp.

The hyporheic zone functions as a critical interface mediating hydrological and biogeochemical exchanges between stream water and streambed. Within shallow streambed layers, sediment transport and biofilm colonization can induce dynamic layered clogging, alter hydraulic conductivity, and foster physical stratification that significantly modulates hyporheic exchange patterns. This study develops a coupled hydrodynamic–mass transport model for a representative streambed bedform to examine the impacts of biofilm-driven dynamic clogging on hyporheic exchange dynamics. Results reveal that dynamic layered clogging reduces pore water velocity and total water flux, causing a 45.1% decline in the total inflow to the hyporheic zone. The transport of non-absorbable solutes exhibits a biphasic pattern: initial rapid penetration transitions to gradual deceleration over time, with dynamic clogging extending the penetration time of the solute center of mass distribution (CMD). Notably, when hydraulic conductivity falls below a threshold (K* < 0.25), CMD penetration time exhibits a positive correlation with hydraulic conductivity, attributed to porosity-induced changes in actual flow velocity. When considering the anaerobic growth in deeper layers, the penetration time become longer because of the clogging present there. This research clarifies the mechanistic connections between biofilm-induced clogging and hyporheic exchange, providing valuable insights for the management of hyporheic ecosystems and the modeling of biogeochemical processes.