Soil aggregate stability measurement is essential to determine soil health status under various conditions. The Mean Weight Diameter (MWD) is the most applied index to express aggregate stability particularly for wet and dry sieving. However, the MWD could generally present results affected by pre-stress aggregate size distribution when remained aggregates after stress are considered for calculation. Therefore, the objective of the present study was to eliminate the similarities between the MWD results and pre-stress aggregate size distribution, which largely affects treatments differentiation. Samples from 145-160 m (lower), 160-169 m (middle), and 169-175 m (upper) elevations differently affected by the Water Level Fluctuation in Three Gorges Reservoir (TGR) and control (>175 m) were exposed to wet shaking stress. Aggregates remained at each sieve opening, aggregates disintegrated/passed through the sieve opening, and small macroaggregates and microaggregates accumulated were recorded. These aggregates were used to determine and compare two indexes (1) using remained aggregates (MWD) and (2) using disintegrated/accumulated aggregates (MWDd/a) based on the differences among treatments. The results for both pre-stress aggregates and remained aggregates after stress were showed consistent significant differences (p < 0.05) between upper and control elevations. This gives indication that aggregates remained after stress strongly depend on pre-stress aggregate size distribution. As the MWD was calculated from remained aggregates, the identified difference between upper and control elevations for this index could also confirm its dependence to pre-stress aggregates distribution. Contrary, disintegrated and accumulated aggregates showed non-significant differences between upper and control elevations. This nonsignificant and significant differences between upper and control elevations for disintegrated and pre-stress aggregates suggest a non-dependence condition. Similarly, the upper and control elevations showed no significant differences in MWDd/a. This substantially informs that this index is independent from pre-stress aggregates distribution because it was entirely calculated from disintegrated aggregates. Higher aggregate stability was indicated by high MWD, with values ranging from 1.41 to 6.24 mm. On the other hand, higher stability was expressed by lower values of the MWDd/a, with the values varying between 3.87 and 0.5 mm. Overall, the present study evidenced the major advantage of considering the disintegrated/accumulated than remained aggregates in calculating unbiased MWD index for aggregate stability.