Between 1932 and 1968, industrial wastewater containing methylmercury (MeHg) and other mercury (Hg) compounds was discharged directly into Minamata Bay, Japan, seriously contaminating the fishery. Thousands of people who consumed tainted fish and shellfish developed a neurological disorder now known as Minamata disease. Concentrations of total mercury (THg) in recent fish and sediment samples from Minamata Bay remain higher than those in other Japanese coastal waters, and elevated concentrations of THg in sediments in the greater Yatsushiro Sea suggest that Hg has moved beyond the bay. We measured stable Hg isotope ratios in sediment cores from Minamata Bay and the southern Yatsushiro Sea and in archived fish from Minamata Bay dating from 1978 to 2013. Values of δ(202)Hg and Δ(199)Hg in Yatsushiro Sea surface sediments were indistinguishable from those in highly contaminated Minamata Bay sediments but distinct from and nonoverlapping with values in background (noncontaminated) sediments. We conclude that stable Hg isotope data can be used to track Minamata Bay Hg as it moves into the greater Yatsushiro Sea. In addition, our data suggest that MeHg is produced in bottom sediments and enters the food web without substantial prior photodegradation, possibly in sediment porewaters or near the sediment-water interface.