Soils excavated in construction works often contain non-anthropogenic heavy metals and metalloids due to their geologic histories. Evaluation of their leaching behaviors is essential to predict the environmental impact and achieve an optimum design when reusing such soils as construction materials. However, applicability of the conventional column leaching test to soils containing non-anthropogenic substances is uncertain, since their chemical forms and leaching processes are different from those in contaminated soils. Also, the column size is one of factors influential to the leaching behavior. This paper addresses the leaching behaviors of arsenic (As) and other inorganic constituents contained in a marine sediment by employing two different-size column percolation tests (50 mm in diameter × 300 mm in height and 150 mm in diameter × 700 mm in height) with saturated/unsaturated flow conditions. Long term leaching profiles were analyzed to assess the effects of specimen size and flow conditions. At the middle of the unsaturated larger column, higher As leaching concentrations were observed under neutral condition. However, As leaching was limited at the bottom due to precipitation of As with co-precipitation of iron and aluminum compounds. As a result, there was no significant difference in both As leaching amount and leaching processes obtained in two column percolation tests.