Recently, researchers in coastal engineering have paid more attention to the role of sediment (particulate organic matter adsorbed on fine solid particles, diameter range 1-m) in considering the biodiversity of estuaries. In this study, permeability reduction of saturated sand columns by sediment retention is investigated through laboratory experiments. Water-based sediment was injected through vertical sand columns under a constant water head difference, with different flow rates, porosities of the sand columns, and the chemical properties of sediment. It was found that the permeability reduction was uniquely correlated with flow rate and sediment properties; that is, increasing flow rate or using sediment containing high amounts of organic matter causes a significant reduction in permeability. Furthermore, an approximate experimental equation is proposed to predict the retention mass of sediment. This equation can predict the retention mass with a relative error of less than 5 %. In addition, a new model is proposed to determine the permeability reduction by sediment retention. This model could predict the permeability reduction with a relative error of 10 %.