The shallow lakes in the middle and lower Yangtze River floodplain are essential wintering grounds, providing abundant food resources and wintering condition guarantee for waterbirds on the East Asian-Australasian Flyway. In recent years, to meet the needs of the residents around the lakes for production and living, many of these shallow river-connected lakes have water levels controlled by dams and sluices in the middle and lower Yangtze River floodplain. The gate-controlled water level is currently the most common hydrological disturbance used in the area. Waterbirds as indicator of wetland ecosystem, exhibit sensitivity to shifts in water levels, and composition in their diversity can elucidate the effects of water level changes on wetland ecosystems. In this study, the impact of water level changes on wintering waterbird communities was investigated based on taxonomic and functional diversity. Over the wintering seasons during 2021-2022 and 2022-2023, field observations of wintering waterbirds were conducted at Wuchang Lake, along with remote sensing data, we obtained the waterbird species, composition, distribution, and habitat factors. Based on the changes in waterbird community composition across interannual water level conditions, we analyzed the effects of habitat changes on wintering waterbird diversity and examined the response of wintering waterbird communities to water level changes. The results indicate that throughout the two wintering years, the waterbirds of order Anseriformes were predominant at Wuchang Lake. Shannon-Wiener diversity index was significantly higher (P < 0.05) during high water year, accompanied by a significant decrease in functional divergence index (P < 0.05). This indicates substantial disparities in species composition, abundance, and trait characteristics between the two wintering years. The results by general linear models revealed that habitat area was affected by water level, with significant correlations (P < 0.05) between water level and shallow water, mudflat, and deep water, but not with emergent plant area (P > 0.05). The results by generalized linear mixed models revealed that the major cause of shifts in waterbird community diversity was habitat changes due to water level changes. Moreover, water level changes also directly impacted the diversity of wintering waterbird communities, with significant correlations noted between the Shannon-Wiener diversity index, the functional richness index, and water levels (P < 0.05). This study elucidated the impact of water level changes on wintering waterbird communities by investigating the interconnections between water levels, waterbirds, and their habitats, thereby providing crucial scientific guidance for the conservation and management of lake ecosystems.