The tidal flat along the Changjiang (Yangtze) River estuary has long been reclaimed for the agricultural purposes, with the prevailing hydrological conditions during such pedogenic transformations being of great importance to their successful development. In this study, samples of surface sediment from Chongming Dongtan, situated at the mouth of the Changjiang River estuary, were collected and analyzed in order to understand how hydrological management can influence the concentrations of heavy metals and salt ions in pore water, and chemical fractionation of heavy metals during the reclamation process. We performed a series of experiments that simulated three different hydrological regimes: permanent flooding (R1), alternative five-day periods of wetting and drying (R2), continuous field capacity (R3). Our results exhibited good Pearson correlations coefficients between heavy metals and salt ions in the pore water for both R1 and R2. In particular, the concentrations of salt ions in the pore water decreased in all three regimes, but showed the biggest decline in R2. With this R2 experiment, the periodic concentration patterns in the pore water varied for Fe and Mn, but not for Cr, Cu, Pb and Zn. Neither the fractionation of Ni nor the residual fractions of any metals changed significantly in any regime. In R1, the reducible fractions of heavy metals (Cr, Cu, Zn and Pb) in the sediment decreased, while the acid extractable fractions increased. In R2, the acid extractable and the reducible fractions of Cr, Cu, Zn and Pb both decreased, as did the oxidizable fraction of Cu. These data suggest that an alternating hydrological regime can reduce both salinity and the availability of heavy metals in sediments.