A flexible riverbed protection called tetrahedron framed permeable weirs (TFPW) is proposed to protect riverbeds in mountainous areas from scouring. Under clear water conditions, a series of laboratory flume experiments were performed to study the effects of TFPW with different layout types on the stability of riverbeds. The objectives of this paper were to advance understanding of the role that TFPW play in the erosion process of river beds and to optimize the TFPW design for reducing velocity, promoting sediment deposition and good structural stability. Data on velocity distribution and variation, equilibrium bathymetry, flow resistance, bed form characteristics and structural stability were collected and analyzed. The results indicate that (1) with good structural stability, all the TFPW with different layout types had significant effects on the stabilization of the riverbed by reducing velocity, raising the water level, increasing the roughness coefficient, protecting the riverbed from degradation and promoting deposition; and (2) the random Double TFPW with large rates of deceleration, large deposition ranges, and good structural stability, and the paved Single TFPW with small rates of deceleration but large deposition ranges and perfect structural stability, were suitable and optimal for riverbed protection in a clear water channel.