The leaching behavior of arsenic (As), lead (Pb), nickel (Ni), iron (Fe), and manganese (Mn) was investigated from subsurface core sediment of marine and nonmarine depositional environments in central Kanto Plain, Japan. A four-step sequential extraction technique was adopted to determine the chemical speciation, potential mobility, and bioavailability of metals under natural conditions in variable depositional environments. In addition, a correlation of these properties with pore water and total metal content was carried out. The concentration of As in pore water was found to be 2–3 times higher than the permissible limit (10 µg/L) for drinking water and leachate in fluvial, transitional, and marine environments. The trend of potential mobile fractions of As, Pb, and Ni showed Fe–Mn oxide bound > carbonate bound > ion exchangeable bound > water soluble in the fluvial environment. However, in the marine environment, it showed Fe–Mn oxide bound > water soluble > carbonate bound > ion exchangeable bound for As. The leaching of As in this fluvial environment is due to the organic matter-mediated, reductive dissolution of Fe–Mn oxide bound, where Mn is the scavenger. The amount of total content of As and sulfur (S) in transitional sediment reflects an elevated level of leachate in pore water, which is controlled by S reduction. However, the leaching of As in marine sediment is controlled by pH and organic matter content.