In Japan, several restorations of rivers have been implemented due to riverbed degradation and vegetation encroachment, which are induced by various factors such as dam construction and past over-exploitation of sediments. Seigyu is one of indigenous traditional river structures in Japan, used for restoring and maintaining riverbanks. This paper investigates the flow patterns and riverbed changes around three units of Seigyu installed on a gravel bar in Kizu River. The flow approaches the Seigyu head with high velocity and creates a mixing zone at the downstream of the Seigyu with low velocities buffer zone. The installed Seigyu structures affected the bed deformation by inducing erosion and deposition locally, as well as the modifications of the habitat structure. The analysis indicates that the Seigyu structures have effective performance in improving sediment erosion and deposition patterns and development of ponds on sandbar for riverine habitat restoration.