A geospatial modeling system may include a geospatial model data storage device and a processor cooperating with the geospatial model data storage device for inpainting seam-smoothed, void-fill data into a void in a geospatial data set for a geospatial region. The processor may select raw void-fill data from the geospatial data set, and generate the seam-smoothed, void-fill data by applying Poisson's equation to the raw void-fill data using boundary conditions based upon data along a corresponding interface between the void region and adjacent portions of the geospatial region.