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Bedform‐driven hyporheic exchange is conditioned by the head gradients at the sediment‐water interface. Local exchange phenomena between the surface and the subsurface are often driven by the dynamic forces related to the velocity distributions around sediment waves. In open channels, the static forces are represented by the water depth, yet most computational fluid dynamics models use a rigid‐lid approximation. We investigated whether and when the deformation of the river's free‐surface influences bedform‐driven hyporheic exchange. This was done through simulations of coupled open‐channel and hyporheic flows with the air‐water interface modeled either as a free‐surface or a rigid‐lid across increasing subcritical Froude numbers from ∼0.05 to ∼0.95. The normalized hyporheic flux was higher when considering free‐surface deformation across most of the range of Froude numbers considered. When the Froude number was larger than 0.6 and smaller than 0.85, both hydrostatic and non‐hydrostatic‐driven fluxes increased significantly compared to the rigid‐lid approach and the total flux was about 5 times that predicted with the rigid‐lid. These results indicate that bedform‐driven hyporheic fluxes are underestimated in most studies that use a rigid‐lid assumption in subcritical flows.

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