Hydrological regimes have been significantly altered since the Three Gorges Dam (TGD) raised the water level of the reservoir to the maximum design level of 175 m in October 2010. This change might greatly influence the forms of phosphorus (P) in the sediment and the adjacent riparian soil. The purpose of this study was to reveal the lateral (sediment, water-level-fluctuation zone soil, and upland soil) and longitudinal (from the end of backwater area to the TGD) trends in P factions. Samples from 11 sites located along the main stem and ten sites located along eight tributaries were collected in June 2017. The P fractions were determined using the Standards, Measurements, and Testing (SMT) protocol. The results showed that the order of increase for average pH values was sediment (7.58 ± 0.62), WLFZ soil (7.44 ± 0.29), and adjacent upland soil (7.20 ± 0.68). The total organic carbon in the sediment was also highest with an average of 9.15 ± 2.97 mg·g. The average concentrated HCl-extractable P (total P), organic P (OP), inorganic P (IP), HCl-extractable P (HCl-P), and NaOH-extractable P (NaOH-P) were 630.02 ± 212.24, 161.89 ± 90.77, 468.13 ± 194.92, 335.65 ± 159.88, and 51.40 ± 36.20 mg·kg, respectively. The concentration of both total P and NaOH-P in the sediment of the main stem exhibited an increasing trend from the backwater area to the TGD. The average concentration of P species in the sediment was higher than those in the upland soil and the water-level-fluctuation zone (WLFZ) soil. For all the sediment and soil samples, the rank order of P species concentrations was HCl-P > OP > NaOH-P. Both IP and HCl-P were highly positively correlated with total P in the upland soil, the WLFZ soil and the sediment. However, only in the sediment, NaOH-P was positively correlated with total P and OP. All P species in the upland soil demonstrated greater spatial heterogeneity than those in the WLFZ soil and the sediment. Redundancy analysis revealed that the main variables explaining the variance in P species concentrations were Al in the upland soil and pH in the sediment.
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