The bay of Green Bay is the world’s largest freshwater estuary in the Laurentian Great Lakes, covering approximately 7% of Lake Michigan’s surface area. Since the 1980s, the lower Fox River-Green Bay has been designated as an Area of Concern due to increased urbanization, industrial activities, and agricultural runoffs. Despite decades of regulations and cleanup efforts, the bay of Green Bay continues to experience eutrophic conditions and frequent seasonal hypoxia. Research over the past several decades has been primarily focused on the assessment and remediation of nutrients and persistent organic pollutants (PCBs and PAHs) in the bay of Green Bay. However, the distributions and deposition history of heavy metals in Green Bay sediments have not been systematically studied. To address this gap, surface and core sediments were collected during a sampling cruise in 2021. Dried sediment samples were acid digested for the measurements of heavy metals, including Cu, Pb, Zn, Cd and Hg using Inductively coupled plasma mass spectrometry. Results indicated distinct distribution patterns of the measured heavy metals in surface sediments. By integrating sedimentation rates established from radionuclide analysis, the pollution and deposition history of these heavy metals was reconstructed based on their vertical concentration profiles. Although the enactment of the Clean-Water-Act in 1970s resulted in a decline in heavy metal concentrations in sediments, overall concentrations of Cu, Pb, Zn, Cd and Hg in Green Bay sediments had generally increased from the 1940s to the present. These findings provide valuable insights into the deposition history and removal processes of heavy metals, offering a scientific basis for remediation effort, environmental management, and policy making related to heavy metal pollution in the bay of Green Bay.