The method of water free surface adapting grid system with 2D structured grids was extended to 3D unstructured grids to simulate phreatic surface in seepage flow. In this approach, the grid system does not need to be modified or regenerated during nonlinear iterations, whereas free surface is mapped to grid nodes to determinate the final phreatic surface without handling seepage face specifically. The good agreement of computations and experimental results indicated that this method can capture the phreatic surface in 3D unstructured grids with well precision. This study extended the application range of adapting grid method in unconfined seepage flow.