After the pollutant discharged into the river or lake has been reduced, the release of the contaminant from the sediment to the overlying water may cause the river and lake be contaminated again. On the condition that the overlying water flow does not lead to sediment suspension, numerical researches are carried out for the mechanism of contaminant release through the sediment-overlying water interface. The overlying water flow is calculated as turbulence. The sediment is regarded as isotropic homogeneous porous medium, therefore the seepage field in the porous sediment layer is obtained by solving Darcy’s equations. Coupled two dimensional steady flows of the overlying water and the pore water in the sediment are calculated. Based on the flow fields obtained, the unsteady contaminant solute transportation process in the pore water in the sediment and the overlying water is numerically simulated, as the shapes of the sediment-overlying water interface are flat or periodic triangular respectively. Numerical results show that the exchange of the pore water and the overlying water is an important factor which decides the release flux of the contaminant from the sediment to the overlying water. The pressure distribution produced by the overlying water flow along the sediment-overlying water interface, as it is not flat, may induce the seepage of the pore water in the sediment and through the sediment-overlying water interface, which may increase the release flux of the contaminant from the sediment to the overlying water.