A 3D split-step Fourier method is presented and tested. It is based on a spectral representation of the discrete wave equation in cylindrical coordinates. The formulations in this method are self-consistent in the discrete domain. This method is applied to simulate the propagation with ducts retrieved after clutter data inversion. In the numerical tests, the difference between N × 2D and 3D models is not significant. Thus, in this case, considering the 3D atmosphere effects is unnecessary.