Beijing is a major metropolis in China, which shows characteristics of significant land subsidence because of long-term overexploitation of groundwater. Since the South-to-North Water Diversion Project Central Route was first operated in December 2014, it has provided Beijing with a new source of water. In this study, a variety of monitoring data has been used to analyze the changes in the groundwater flow field and land subsidence when comparing the conditions before and after the Water Diversion Project started, and to study the stress-strain characteristics of the soil layers at different depths under different water-level-change modes. Meanwhile, causes of the large residual deformation and hysteresis deformation of the cohesive soils are discussed. The study reveals that after the operation of the Water Diversion Project, the area of the groundwater depression cone and the rate of land subsidence in the Beijing Plain showed an overall decreasing trend. The deformation characteristics of different lithological soil layers under different water-level-change modes can be summarized into four categories. The sand layer is mainly characteristic of elastic deformation. The cohesive soil layers of different depths have elastic, plastic and creep deformation, and the viscoelastic-plastic characteristics are obvious. The large residual deformation and hysteresis deformation of the cohesive soil layer are mainly caused by two factors: firstly, the inelastic water storage rate is greater than the elastic water storage rate, and secondly, the cohesive soil has weak permeability.