Industrial chemical contamination within coastal regions of the Great Lakes can pose serious risks to wetland habitat and offshore fisheries, often resulting in fish consumption advisories that directly affect human and wildlife health. Mercury (Hg) is a contaminant of concern in many of these highly urbanized and industrialized coastal regions, one of which is the Saint Louis River estuary (SLRE), the second largest tributary to Lake Superior. The SLRE has legacy Hg contamination that drives high Hg concentrations within sediments, but it is unclear whether legacy-derived Hg actively cycles within the food web. To understand the relative contributions of legacy versus contemporary Hg sources in coastal zones, Hg, carbon, and nitrogen stable isotope ratios were measured in sediments and food webs of SLRE and the Bad River, an estuarine reference site. Hg stable isotope values revealed that legacy contamination of Hg was widespread and heterogeneously distributed in sediments of SLRE, even in areas lacking industrial Hg sources. Similar isotope values were found in benthic invertebrates, riparian spiders, and prey fish from SLRE, confirming legacy Hg reaches the SLRE food web. Direct comparison of prey fish from SLRE and the Bad River confirmed that Hg isotope differences between the sites were not attributable to fractionation associated with rapid Hg bioaccumulation at estuarine mouths, but due to the presence of industrial Hg within SLRE. The Hg stable isotope values of game fish in both estuaries were dependent on fish migration and diet within the estuaries and extending into Lake Superior. These results indicate that Hg from legacy contamination is actively cycling within the SLRE food web and, through migration, this Hg also extends into Lake Superior via game fish. Understanding sources and the movement of Hg within the estuarine food web better informs restoration strategies for other impaired Great Lakes coastal zones.