Spatial hydrological alterations can affect soil structural stability. Over time, forces induced by water weaken soil aggregates and this has a negative implication to soil health. The Three Gorges Reservoir (TGR) in particular, experienced a long-term hydrological condition and repetitive seasonal water level fluctuations that could affect soil health. The present study was conducted to investigate the effects of different water levels on soil aggregate disintegration rate over time and its relation to soil erosion susceptibility in water reservoirs. Samples from different elevations (155 m, 160 m, 163 m, 166 m, 172 m, and 180 m) in the water level fluctuation zone (WLFZ) were exposed to continuous wet-shaking for 3, 9, 27, 54, and 81 min resulted to different WLF intensity accordingly. The results showed a comparative difference between aggregates size before and after the experi-ment where micro-aggregates (<0.25 mm) increased with respect to elevations increase. The exponential pre-diction proved that aggregate stability decreased with the increase of WLF intensity, insisting the effects of continuous hydrological stress to aggregate break-down. A couple of factors definitely confirmed that soil erodibility (k) is primarily determined by disintegration of soil aggregates for the surface soil of the TGR. Despite the fact that Disintegration rate (Dr) and k showed a positive relationship, R2 = 0.73 (p < 0.05), the results showed that the soil properties decreasing Dr also decreases soil erodibility in the study area. Non-effective role of soil organic matter (SOM) for stabilizing soil aggregates was primarily related to water level fluctuations inhibiting decomposition. Relying on the present findings, environmental problems mostly soil erosion in the TGR could be therefore linked to excessive destabilization of soil aggregates. Therefore, the results of this study should play a major role in determining the factors primarily inducing soil erosion in river reservoirs.