The purpose of this study was to examine the dynamics of the chemical properties of soil in the water level fluctuating zone of the Three Gorges Reservoir (TGR) region. In addition, the potential impact of vegetation reconstruction on water quality was investigated. Bald cypress (Taxodium distichum) and Chinese willow (Salix matsudana) are the two dominant species in the riparian zone of the TGR area. Soil samples were taken from vegetation planted below either T. distichum, S. matsudana (treatments), or bare soil (control) in July 2012 (T1) and July 2013 (T2), before flooding and after water flooding respectively. The following parameters were measured:soil pH, organic matter (OM), alkali hydrolysable nitrogen (AN), available phosphorus (AP), available potassium (AK), total nitrogen (TN), total phosphorus (TP), total potassium (TK), and plant growth. The results showed that:(1) At T1, the treatment and control soil nutrient contents were significantly different, whilst pH did not differ between these groups. In contrast, at T2, only the pH, AP, TP, and AK showed significant differences between the treatments and control. (2) The pH value and OM content of T. distichum in T2, as well as OM content in S. matsudana in T2, were significantly lower than those in T1. After flooding (T1), although AN, AP, and TK contents below the experimental vegetation were significantly lower than the control, TP content was significantly increased. In contrast, at T2, besides an obvious decrease of AN content and a significant increase in AK, the other nutrient elements did not have any notable differences. (3) Correlation analysis showed that pH values were negatively correlated with TP, and OM showed a positive correlation with AN, AP, and TK. Furthermore, AN and AP were negatively correlated with TP and positively correlated with TK. TP and TK had a strong negative relationship. The three growth indices including height, diameter at breast height (DBH), and canopy cover were negatively correlated with soil nutrient elements, including pH, OM content, AN, AP (except height), and TK, while the height showed a positive correlation with TP. In conclusion, this study suggests that the effects of artificially vegetating soil appear only before flooding (T1), but no tafter water flooding (T2). Soil chemical properties under different treatments were homogeneous, which further confirms that artificial revegetation can improve the soil ecological environment with a low chance of eutrophication of the water body. However, there is the potential risk of phosphorus being released from the revegetation soil under S. matsudana, and therefore the detection of water phosphorus content is an important factor to take into consideration.