A geospatial modeling system may include a geospatial model data storage device, and a processor cooperating with the geospatial model data storage device for merging first and second geospatial data sets for corresponding first and second geospatial regions. The processor may be for generating seam-smoothed geospatial data for a corresponding selected geospatial region between adjacent portions of the first and second geospatial regions by applying Poisson's equation to data from at least one of the first and second geospatial data sets for the selected geospatial region using boundary conditions based upon data along corresponding interfaces between the selected geospatial region and adjacent portions of the first and second geospatial regions.