Carbon (C), nitrogen (N), and phosphorus (P) stoichiometry serve as valuable indices for plant nutrient utilization and biogeochemical cycling within ecosystems. However, the allocation of these nutrients among different plant organs and the underlying drivers in dynamic riparian ecosystems remain inadequately understood. In this study, we gathered plant samples from diverse life forms (annuals and perennials) and organs (leaves, stems, and roots) in the riparian zone of the Three Gorges Reservoir Region (TGRR) in China—a novel ecosystem subject to winter flooding. We used random forest analysis and structural equation modeling to find out how flooding, life forms, plant communities, and soil variables affect organs C, N, and P levels. Results showed that the mean concentrations of plant C, N, and P in the riparian zone of the TGRR were 386.65, 19.31, and 5.27 mg/g for leaves respectively, 404.02, 11.23, and 4.81 mg/g for stems respectively, and 388.22, 9.32, and 3.27 mg/g for roots respectively. The C:N, C:P and N:P ratios were 16.15, 191.7 and 5.56 for leaves respectively; 26.98, 273.72 and 4.6 for stems respectively; and 16.63, 223.06 and 4.77 for roots respectively. Riparian plants exhibited nitrogen limitation, with weak carbon sequestration, low nutrient utilization efficiency, and a high capacity for nutrient uptake. Plant C:N:P stoichiometry was significantly different across life forms and organs, with higher N and P concentrations in leaves than stems and roots, and higher in annuals than perennials. While flooding stress triggered distinct responses in the C, N, and P concentrations among annual and perennial plants, they maintained similar stoichiometric ratios along flooding gradients. Furthermore, our investigation identified soil properties and life forms as more influential factors than plant communities in shaping variations in C:N:P stoichiometry in organs. Flooding indirectly impacts plant C:N:P stoichiometry primarily through alterations in plant community composition and soil factors. This study underscores the potential for hydrologic changes to influence plant community composition and soil nutrient dynamics, and further alter plant ecological strategies and biogeochemical cycling in riparian ecosystems.