In Japan, the amount of freshwater and short-neck clams imported from countries, such as China, South Korea, and North Korea, has increased with the decrease in their domestic production. This calls attention to the contamination of marketed clams with toxic substances, such as heavy metals in aquatic environments, from the viewpoint of food safety and security, because their origin has been falsely indicated. Herein, first, we measured the concentrations of Cd, Cu, Pb, and Zn in marketed freshwater and short-neck clam samples to clarify the extent of their contamination. Consequently, we found that some of the freshwater clam samples were contaminated with both Cd and Pb at concentrations comparable to their maximum concentrations in bivalve mollusks imposed by the Commission of the European Communities. Further, we evaluated the sources of Pb in the contaminated clams on the basis of Pb isotope ratios. The result supported the hypothesis that the Pb in the contaminated freshwater clam samples originates predominantly from effluent and exhaust from mining or smelting, which is associated with old Pb ores formed in some countries, such as China and North Korea. On the contrary, it appears that the contamination of freshwater clam samples with Cd is attributable to the Cd contained as an impurity in effluent and exhaust from the mining or smelting.