Human activity is the major factor driving the wetland degradation in shallow lakes. Human exploitation of lake wetlands alters the habitats of wintering waterbirds, and, in turn, waterbird diversity in the shallow lakes. In the present study, we surveyed species composition, abundance, and habitat characteristics of waterbirds in three types of wetland habitats (natural lakeside wetlands, paddy fields, and aquaculture ponds) at Caizi Lake, a shallow lake in the middle and lower Yangtze River during the wintering period, and investigated the effects of habitat change driven by human activity on the diversity of wintering waterbirds. There were significant differences in species composition and abundance among the three wetland habitats (natural lakeside wetlands, aquaculture ponds, and artificial paddy fields); however, there were no significant differences among the habitats with respect to the number of waterbirds. The numbers of overwintering waterbird species and waterbird individuals in aquaculture ponds and lakeside wetlands were significantly higher than the numbers in the paddy fields, indicating that wintering waterbirds prefer natural lake wetlands and aquaculture ponds. Principal component analysis of the three wetland habitat types revealed that factors influencing waterbird diversity include wetland area, vegetation cover, water level, and degree of human interference. Therefore, minimizing human interference and ensuring suitable habitats at specific periods could facilitate the maintenance of waterbird diversity.