The altered water regime and cadmium pollution in the Three Gorges Reservoir of the Yangtze River, China, has caused many serious environmental problems. Consequently, it is of great importance to restore the riparian vegetation and soil. Salix variegata is potentially a suitable species for the phytoremediation of Cd-contaminated areas under environmental flooding conditions. To determine the microorganism community and enzymatic activity in Cd-contaminated soils under flooding conditions, an experiment with a factorial design was conducted. Treatments included two water regimes and four Cd concentrations. The water treatments were ambient water supply (CK) and light flooding (FL). In terms of cadmium, there was a control (0 mg/kg), and cadmium treatments with low (0.5 mg/kg), moderate (2 mg/kg), and high concentrations (10 mg/kg). Each cadmium treatment was conducted with and without S. variegata. Soil samples were collected on the 60^th and 120^th day following treatment, and the characteristics of soil microorganisms and enzymatic activities were determined. The results showed that: (1) S. variegata plantings significantly increased the quantity of bacteria in the soils on the 60^th day (P < 0.05) and slightly increased the quantity of actinomycetes and fungi. (2) The quantity of soil microorganisms under flooding conditions was much lower than that in the normal water supply groups. Flooding significantly decreased the quantity of bacteria and fungi on the 60^th day, and the quantity of actinomycetes and fungi on the 120^th day compared with that of the normal water supply groups (P < 0.05). (3) The Cd treatments had little effect on the quantity of soil microorganisms (P > 0.05). The primary reason may be the relatively low concentrations of Cd in this study. (4) Planting S. variegata significantly improved the activity of phosphatase in the soils on the 60^th day and the activities of urease and invertase in the soils on the 120^th day (P < 0.05). (5) The activity of phosphatase on the 60^th day, and the activity of urease, invertase, and phosphatase on the 120^th day were significantly reduced by flooding. (6) The activity of phosphatase on the 60^th day and the activity of urease on the 120^th day were significantly reduced by Cd stress. In summary, microorganisms and enzymatic activity in soils, which were sensitive to Cd stress and flooding, could be used to estimate the effect of phytoremediation on Cd-contaminated soils in the riparian area of Three Gorges Reservoir. Planting S. variegata could improve the status of microorganisms and enzymatic activity in Cd-contaminated soils under flooding conditions. S. variegata has significant potential to improve Cd-contaminated soils in a flooded environment.