Vertical distribution processes of sediment contaminants in water were studied by flume experiments. Experimental results show that settling velocity of sediment particles and turbulence characteristics are the major hydrodynamic factors impacting distribution of pollutants, especially near the bottom where particle diameter is similar in size to vortex structure. Sediment distribution was uniform along the distance, while contaminant distribution slightly lagged behind the sediment. The smaller the initial sediment concentration was, the more time it took to achieve a uniform concentration distribution for suspended sediment. A contaminants transportation equation was established depending on mass conservation equations. Two mathematical estimation models of pollutant distribution in the overlying water considering adsorption and desorption were devised based on vertical distribution of suspended sediment: equilibrium partition model and dynamic micro-diffusion model. The ratio of time scale between the sediment movement and sorption can be used as the index of the models. When this ratio was large, the equilibrium assumption was reasonable, but when it was small, it might require dynamic micro-diffusion model.