A method and a system are for three-dimensional (3D) synthetic aperture (SA) imaging. The method and system use spatial modulation on SA return signals as a function of their return angle distribution to account for local topography and provide 3D imaging capabilities. In some implementations, the method can involve a step of generating two spatially modulated two-dimensional (2D) SA images of a target region, each of which having a different spatial modulation profile, and a step of combining the two spatially modulated 2D SA images to obtain a 3D SA image. The 3D SA image can be used to determine an elevation map of the target region.