This study presents a numerical solution to the three-dimensional solute transport in heterogeneous media by using a layer-integrated approach. Omitting vertical spatial variation of soil and hydraulic properties within each layer, a three-dimensional solute transport can be simplified as a quasi-three-dimensional solute transport which couples a horizontal two-dimensional simulation and a vertical one-dimensional computation. The finite analytic numerical method was used to discretize the derived two-dimensional governing equation. A quadratic function was used to approximate the vertical one-dimensional concentration distribution in the layer to ensure the continuity of concentration and flux at the interface between the adjacent layers. By integration over each layer, a set of system of equations can be generated for a single column of vertical cells and solved numerically to give the vertical solute concentration profile. The solute concentration field was then obtained by solving all columns of vertical cells to achieve convergence with the iterative solution procedure. The proposed model was verified through examples from the published literatures including four verifications in terms of analytical and experimental cases. Comparison of simulation results indicates that the proposed model satisfies the solute concentration profiles obtained from experiments in time and space.