This study uses factorial and indicator kriging methods with a geographic information system (GIS), to overlay and delineate the variation and pollution sources of soil heavy metals in fields in the north of Changhua County, Taiwan. Accordingly, the spatial variation and pollution probability patterns of soil cadmium, chromium and copper are estimated to support further environmental monitoring, remediation and planning. The overlay maps of industrial plants, irrigation channels and kriging estimates, constitute a GIS. This reveals that the short- and long-range variations and soil pollution by Cd, Cr and Cu strongly corresponded to the locations of irrigation systems and industrial plants in the area of study. The maps also verify most locations of suspected pollution sources from the GIS database. Moreover, the probability spatial patterns estimated by indicator kriging, based on the pollution thresholds of Cd, Cr and Cu, were also highly correlated with irrigation channels and industrial plants. The GIS, with factorial and indicator kriging under different combinations of variations and pollution probabilities of soil Cd, Cr and Cu, provide alternative scenarios for delineating the areas that contain high variation and high pollution probability of these heavy metals, to enable decision makers to identify pollution sources, and to further investigate and remedy soil pollution.