Biomimetic pumps can effectively enhance the hydrodynamics of plain river networks, improve the water environment, and facilitate the transport of sticky bottom sediment. In this paper, a biomimetic pump equipped with an NACA0012 wing profile was used as the research subject, and a commercial CFD package was employed to investigate the impact of the pump’s installation height (the vertical distance from the hydrofoil’s pivot to the riverbed) and operating frequency on the incipient motion of riverbed sediment. The results indicate that the lowest maximum near-bed velocity is obtained at an installation height of 3 times the chord length (3 c) and operating frequency of 0.5 Hz, while the highest is reached at 4 c and 5 Hz. The maximum near-bed velocity point is the furthest from the biomimetic pump when the installation height is 3 c and the operating frequency is 0.5 Hz and the closest at 4 c and 0.5 Hz. At a fixed installation height, a quadratic relationship is found between the maximum near-bed velocity and the operating frequency. At installation heights of c, 2 c, and 4 c, the effect of operating frequency on the point of action is minimal, with only a sudden change followed by stability at 3 c as the frequency increases. When the operating frequency is fixed and the installation height is increased, the maximum near-bed velocity initially decreases and then rises, being the smallest at 3 c. The distance between the point of maximum near-bed velocity and the biomimetic pump initially increases and then decreases with increasing installation height, being the farthest at 3 c. Furthermore, in this paper, we fitted mathematical expressions for the maximum near-bed velocity relative to the operating frequency under different installation heights of the biomimetic pump and calculated the threshold frequencies for the incipient motion of sediment at installation heights of c, 2 c, 3 c, and 4 c to be 1.15 Hz, 1.64 Hz, 2.85 Hz, and 1.06 Hz, respectively, providing scientific guidance for the application of biomimetic pumps in various scenarios.