Heavy metal elements, including Zn, Cd, As, Ni, Cu, Pb and Cr, were detected in soils (no deeper than 75 m) from newly reclaimed zones of Shanghai, China. The Zn concentration exceeded soil quality limits. The Zn contamination was tested in both dredger fills and sedimentary layers (①_3-3, ②₃, ④ and ⑤_1-1). However, it was not detected in layer ⑤_1-2-⑨. PCA and HCA analysis show that exogenous Zn probably was the contaminant source of dredger fills before the fills were dredged from the neighboring waters. Stochastic heterogeneity of the dredger fills affects the Zn-depollution remarkably. Numerical simulations show both acid precipitation and widespread drainage channels in the zones contributed to Zn-decrease in the dredger fills no deeper than 1.2 m. Acid rainstorms work better than acid constant precipitation in Zn-remediation for layers below 0.4 m. To remove Zn contamination in deep dredger fills, un-consolidation of the fills should be utilized.