<p>The anti-seasonal hydrological alternation in the Three Gorges Reservoir (TGR) significantly impacts the release of phosphorus (P) from the riparian soil-plant system, posing a threat to the aquatic environment. To investigate this issue, riparian soils and plants in three tributaries of the central TGR were sampled at three distinct stages: early exposure, final exposure, and soon after inundation receded. Soil properties, P forms, and plant P content were analyzed. A significant decrease in exchangeable P and organic P during exposure, and a decrease in aluminum/iron-bound P during inundation were observed. These changes were linked to the mineralization of organic matter and the reduction of iron oxides. Compared to bioavailable inorganic P, bioavailable organic P contributed more to the total soil P release during the exposure-inundation cycle. Plant P uptake accounted for 76.08% of the bioavailable P released by the soil during exposure. During inundation, plant P release significantly exceeded soil P release. Therefore, the soil-plant system could act as a P “sink” during exposure and a P “source” during inundation. The hydrological alternation of the TGR was the primary driver of this “source-sink” transformation. To mitigate P release in riparian zones, recycling plant materials and establishing monitoring sites are recommended.</p>