Groundwater vulnerability mapping in the Bantul area, Yogyakarta was carried out to highlight water resources at risk and to identify vulnerable zones that require careful management in the area. In order to meet these objectives, an investigation using statistical approach was suggested to inquire the relationship between contaminants concentration (total organic carbon and heavy metals) in groundwater, land use and the intrinsic vulnerability of groundwater. The object of study of this analysis is 30 water samples from 30 shallow wells in the area. This study is generated from the analysis of a well-established Geographic Information System combined with the GOD method (groundwater occurrence, overall aquifer class, depth to groundwater). The results of the GOD parameters calculation produce a range of vulnerability index values from 0.084 to 0.7. In general, the intrinsic groundwater vulnerability of the study area was divided into four classes viz. very low, low, moderate and high. Most of the study areas (84.64%) located in high intrinsic groundwater vulnerability index while the other 15.36% of the study area especially the eastern part are located in very low to moderate vulnerability. The high groundwater vulnerability area is characterized by unconfined aquifers with shallow groundwater depth (0.15 -10.7 meter below ground surface) and overlying lithology such as grainstone, marl and alluvium. Despite being dominated by high vulnerability index, statistical analysis shows the correlation between contaminant load, land use and intrinsic groundwater vulnerability are not significant. The most recent data indicated the groundwater vulnerability index in the study area is more influenced by geogenic factors than anthropogenic factors. This approach may facilitate the regular evaluation needed to determine the impact of dynamic anthropogenic activities, regardless of the future groundwater abstraction strategy.