Ecological decline in the water level fluctuating (WLF) zone of the Three Gorges Reservoir (TGR) has been well established over the past decades. However, the effect of heavy metal fractions present in the sediment and their potential ecological risk under the anti-seasonal hydrological regime are still unclear. The Pengxi River is a tributary of the Yangtze River and it has a typical annual water level fluctuation ranging from 145 to 175 m above sea level. The current study examined heavy metal fractions in sediments containing Cr, Cd, Cu, Pb and Mn collected along the WLF zone using the Tessier sequential extraction scheme. The total organic carbon (TC), total nitrogen (TN), carbon/nitrogen ratio (C/N), pH, particle size composition and content of nitrate (NO3−-N), and ammonium (NH4+-N) differed dramatically among the sampled altitudes and depths and was significantly correlated with the flooding time of the WLF zone. At lower altitudes of the WLF zone, the amounts of the exchangeable (EXC), carbonate-bound (CA) and total heavy metal contents of the surface sediment were much higher compared to those of higher altitudes of the WLF zone. The risk assessment code (RAC) for Cd and Mn showed an opposite trend to that of Cr, Cu, and Pb and mainly depended on the organic matter-bound fraction (OM). The modified RAC (mRAC) indicated a very high potential adverse effect for the whole WLF zone, although the risk value was much lower at the lower altitudes and upper depths of the WLF zone. Our results showed that the positive response of the loosely bound fractions (LOS) of heavy metals to the drought-rewetting (DRW) process minimizes the risk of heavy metals in the WLF zone sediment. © 2017 Elsevier B.V.