The study of hydraulic characteristics of water flow affected by blocked sediment is vital to assess discharge capacity in pipes with sediment sand to understand the process of pollutant and fine sand aggregation. The aim of this paper is to study the blocking effect of permeable sediments on non-full flow in circular pipe and to analyze hydraulic characteristics with backwater. Experiments and numerical simulations were performed and the porous media model is used to simulate the flow in permeable blocked sediments. To evaluate the degree of congestion, the backwater ratio β is proposed. The backwater ratio is positively proportional to blocked sediment height and inversely proportional to blocked sediment particle size and flow value. Cross-sectional velocity in the backwater zone decreases significantly and tends to be uniform as backwater ratio increases. Furthermore, the development of secondary flows and velocity distributions influenced by backwater height is discussed. The dimensionless shear velocity in backwater zone shows an exponential decrease as the backwater ratio increases, which greatly increases the possibility of further sediment deposition.