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The current study aims to assess the contamination level of heavy metal in the shallow aquifer of groundwater in Pati and Rembang coastal areas. The analysis result indicated that arsenic and mercury were detected in the groundwater in the range 0.004 µg L−1 and 0.115-0.310 µg L−1, respectively. Referred to the standard of the heavy metals contents in the consumption water by WHO and Indonesian Water Quality Standard for Ground Water (IWQS), groundwater of coastal areas in Pati and Rembang Regions were polluted by arsenic and mercury. The result has confirmed the existence of arsenic and mercury pollution of some shallow groundwater flow in the coastal areas of Pati and Rembang.