Ruditapes philippinarum is a popular edible clam that occurs densely on the sandy tidal flats on the Japanese coast. However, on the tidal flats in Ariake Bay in Kumamoto Prefecture, western Japan, the clam suffered from extremely high mortality just after settlement on the sediment and this mortality seriously affected the population persistence of the clam. In this study, we focused on the negative impact of manganese in the sediment on the juvenile clam. We surveyed manganese ion concentration in the interstitial water of the sediment on three different sandy tidal flats facing Ariake Bay in Kumamoto Prefecture and one in the west coast of Korea. We conducted laboratory experiments exposing juvenile clam just after settlement to different contents of manganese dioxide in the sediment or manganese ion in the water: with sand containing high content of manganese dioxide (2,300 mg kg⁻¹ dry sediment; henceforth Experiment 1); with seawater containing 5.4 mg L⁻¹ of manganese ion (Experiment 2); and with natural sand and seawater containing 5.4 mg L⁻¹ of manganese ion (Experiment 3). Significant mortality was not noted in Experiment 1 or in Experiment 2, while high mortality was seen in Experiment 3. In the field survey, we detected manganese ion concentration in the interstitial water at only 2.78 mg L⁻¹ on the Arao Tidal Flat. However, we confirmed that manganese ion concentration in the interstitial water became more than 40 mg L⁻¹ in the extraction test with the sediment on the Arao Tidal Flat. These results indicate that manganese ion liquated from the sediment into the interstitial water, due to reduction of manganese oxide, may influence seriously the physiology of juvenile clams on the tidal flats.