This study investigated the effect of how water availability influences the pH and nutrient content of soils planted with two-year-old Dawn Redwood (Metasequoia glyptostroboides) saplings, by applying different water treatments to simulate the water-level-fluctuation zone of the Three Gorges Reservoir in this study. The treatments involved 3 phases. In the first phase, the treatments were presented with a conventional water supply (C), half flooding (H), and full flooding (F). Light drought was introduced in the second phase, and included six: conventional water supply (C), half flooding (H), full flooding (F), conventional water supply followed by light drought (CD), half flooding followed by light drought (HD), and full flooding followed by light drought (FD). In the third phase, all treatments were returned to the conventional water supply. Each treatment group lasted 166 days in total, and contained soil samples planted with two-year-old M. glyptostroboides saplings and soils without vegetation. The pH value, organic matter (OM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkali hydrolysable nitrogen (AN), available phosphorus (AP), and available potassium (AK) content in soils containing M. glyptostroboides soils and non-vegetated soils were measured after each 166-day treatment. After phase I, compared to non-vegetated soils (control), M. glyptostroboides soil in groups C and H had highly significant lower nitrogen and TP content and the H treatment had lower AP content, while the F treatment had higher nitrogen and TP content. Compared with the control (group C), flooding treatment increased the pH value and content of OM, whereas AP content decreased. Compared to the control, the TN, TP, and AN content in group H of M. glyptostroboides soils increased by 17.1%, 16.9%, and 34.2%, respectively. After the drought treatment of phase II, flooding had a significant effect on the subsequent sensitivity of pH value, as well as OM, AN, and AP content in M. glyptostroboides soils. Compared to the control, the OM content in the soils of all the water treatment groups (excluding group C) increased significantly in the soils planted with M. glyptostroboides. Concurrently, compared with group C, the pH value increased by 2.6% and 3.8% in group H and F, respectively;however, the OM content was not significantly different in M. glyptostroboides soils. After the water supply was resumed to the level of the control for all treatments, compared to the control, the pH value of M. glyptostroboides soils in group H and HD decreased. In contrast, the OM content in the soils of all the flooding treatment groups and the TN content in soils of group C and CD content increased significantly. In addition, compared to the control, the OM content significantly increased in all the previous flooding treatment groups. The pH value and a number of nutrient contents under the flooding treatments recovered to the level of the control group after recovery growth treatment. All of the chemical properties of the HD and FD groups in M. glyptostroboides soils also recovered to the level of the CD group. The correlation analysis of soil chemical properties in M. glyptostroboides saplings soils showed that a very significant, positive correlation was present among OM, TP, TN, and AN content. However, the pH value exhibited a highly negative relationship with OM, TN, TP, and TN content. The results showed that M. glyptostroboides is viable for revegetating the water-level-fluctuation zone of the Three Gorges Reservoir, but that timely irrigation during the drawdown time period is necessary.