The upstream cascade reservoirs and the implementation of soil and water conservation practices have effectively mitigated sediment inflow to the Three Gorges Reservoir (TGR) since it was fully operational in 2010. However, total deposited sediments and algal blooms in its tributaries have increased during the post-TGR period. To investigate the spatial distribution characteristics of deposited fractional phosphorus in sediments and its influencing factors, column sediment and overlying water datasets collected from field campaigns were analysed using the multivariate statistical approaches by Partial Triadic Analysis (PTA) and Redundancy Analysis (RDA). The results revealed that fractional phosphorus within the top 20 cm of the column sediment exhibited a distinct vertical structure, and the mean contents of total phosphorus (TP), inorganic phosphorus (Inorg-P) and calcium-bound phosphorus (Ca-P) contents were significantly higher than those measured in the deeper layer. Additionally, fractional phosphorus in the mainstream and estuary sections showed longitudinal distribution patterns. Inorg-P and Ca-P were prevalent in the upstream reaches, while the organic phosphorus (Org-P) and iron-aluminium-bound phosphorus (Fe/Al-P) were enriched in the lower mainstream and estuary regions. Sediment TP reached the highest level in the middle river reach. Multivariate regression via the RDA and variance partitioning indicated that environmental factors of the overlying water were significantly correlated with surface sediment phosphorus levels (R