A simplified numerical model of groundwater and solute transport is developed. At large scale area there exists a big spatial scale difference between horizontal and vertical length scales. In the resultant model, the seepage region is particularly divided into several virtual layers along the z direction and vertical 1-D columns covering x-y 2-D urea according to stratum properties. The numerical algorithm is replacing the full 3-D water and mass balance analysis as the 2-D Galerkin finite element method in x- and y-directions and 1-D finite differentiul approach in the z direction. The reasonable method of giving minimum thickness is successfully used to handle transient change of water table, drying cells and problem of rewetting. The solution of the simplified model is preconditioned conjugate gradient and ORTHOMIN method. The validity of the developed 3-D groundwater model is tested with the typical pumping and backwater scenarios. Results of water balance of the computed example reveal the model computation reliability. Based on a representative 3-D pollution case, the solute transport module is tested against computing results using the MT3DMS. The capability and high efficiency to predict non-stationary situations of free groundwater surface and solute plume in regional scale problem is quantitatively investigated. It is shown that the proposed model is computationally effective.