The water-level fluctuation zone (WLFZ) in the Three Gorges Reservoir (TGR) has attracted significant attention because of its pivotal role in shaping environmental processes. However, with the increasing water level, the effects of nitrogen and phosphorus release from submerged soil–plant systems in the WLFZ on the deterioration in water quality remain poorly understood. In this study, a simulation experiment was conducted involving submerged undisturbed soil columns that was submerged once a year at different elevations (150, 160, and 170 m) before reservoir impoundment in the WLFZ within the TGR area. The results revealed that the concentrations of various forms of nitrogen and phosphorus in the overlying water released after system submergence first decreased, then rapidly increased after 30 days, and reached equilibrium after 120 days of flooding. Particulate N accounted for approximately 70% of the total nitrogen (TN) released, while particulate P accounted for more than 90% of the total phosphorus (TP) released by soil–plant systems after submergence for 200 days, which may be related to soil erosion and plant decomposition. The amounts of N and P released were significantly negatively correlated with the initial mass of the soil–plant system, indicating that nutrient release by the system is more susceptible to submerged soil than to submerged plants. During the flooding period of the WLFZ in the TGR, the release loads of soil–plant systems into reservoir water were 159.83 kg N ha⁻¹ and 19.30 kg P ha⁻¹. These results suggest that soil and plants in the WLFZ of the TGR could be at risk for water-induced deterioration. Therefore, additional vegetation management might be implemented to alleviate water eutrophication in the TGR caused by submerged soil and plants in the WLFZ.