Abstract: The water level fluctuating zone (WLFZ) is a transition belt between the water area and the terrestrial habitat that plays an indispensable role in the water environment. Pengxi River basin with the largest WLFZ area was chosen as the study area. The soils in the WLFZ and the coastal soil samples were collected to analyze the speciation characteristics of heavy metals. Besides, we have evaluated the pollution degree of such metal contaminants as well as the levels of the potential ecological risks with the methods of geo-accumulation index and the risk assessment code (RAC). The average contents of Pb, Cu, Cr, Cd, Zn and Ni in the soils of WLFZ were 68.70, 36.96, 55.10, 0.68, 108.26 and 31.68 mg/kg, respectively. The pollution degree is in the order of Cd > Pb > Zn > Cu > Ni > Cr, among which Cd and Pb pollution were prominent, generally higher than that in soils of mainstream of the Yangtze River and much higher than that in soils of Chongqing area. The RAC value of Cd was 20.62%, showed moderate pollution, and was mainly found in exchangeable and carbonates fraction. The RAC value of Pb, Cu, Cr, Zn and Ni were 5.45%-10.0%, showed low pollution, and were mainly found in residual fraction, accounting for 54.69%-83.05% in the total amount. Compared with the coastal soils, the content of heavy metals was increased in WLFZ soil, but the increased amount of each heavy metal was different. According to fractionation studies, residual fraction was the main part of the increased Cr and Ni. Nevertheless, the main part of the increased Cd, Pb and Zn were found in non-residual fractions. The results of our investigation indicated that under the effect of the terrestrial and aquatic pollution sources, the heavy metals contaminants in the Pengxi River basin were translocated from the coastal soil to the WLFZ, then deposited and enriched.