A three-dimensional numerical model has been developed to simulate stratied ows with free surfaces. The model is based on the Reynolds-averaged Navier-Stokes (RANS) equations with variable-uid density. The equations are solved in a transformed-coordinate system with the use of operatorsplitting method (Int. J. Numer. Meth. Fluids 2002; 38: 1045-1068). The numerical model is validated against the one-dimensional diusion problem and the two-dimensional density-gradient-ow. Excellent agreements are obtained between numerical results and analytical solutions. The model is then used to study transport phenomena of dumped sediments into a water body, which has been modelled as a strongly stratied-ow. For the two-dimensional problem, the numerical results compare well with experimental data in terms of mean particle falling velocity and spreading rate of the sediment cloud for both coarse and medium-size sediments. The model is also employed to study the dumping of sediments in a three-dimensional environment with the presence of free surface. It is found that during the descending process an annulus-like cloud is formed for ne sediments whereas a plate-like cloud for medium-size sediments. The model is proven to be a good tool to simulate strongly stratied free surface ows. Copyright.