This study was initiated to examine if variations in the concentrations of cadmium (Cd) and lead (Pb) in water environment may affect metal levels in local foods and body burden of local residents in non-polluted areas in Japan. Two nationwide databases have been made available on concentrations of Cd in locally harvested brown rice and of Cd and Pb in sediments in local river beds. These data were combined with published data on metal concentrations in polished rice, food duplicates, and blood and urine from the residents. Cd in river sediments correlated significantly with those in brown rice, food duplicates, blood, and urine. Cd in food duplicates correlated with Cd in rice. In contrast, Pb concentrations in the river sediments either did not correlate or correlated only weakly with Pb in biological materials or food duplicates. Possible implication of the different behavior between Cd and Pb regarding the intensity of correlation was discussed with reference to the different routes of exposure to the elements. In conclusions, the Cd body burden on local residents in Japan is significantly influenced by Cd levels in water in the general environment, whereas water-borne Pb did not show clear correlation with the Pb body burden.