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Caisang Lake, a human-modified wetland, experienced dramatic habitat alterations from the planting of lotus and culturing of crab. Whether the Caisang Lake still maintains populations of wintering waterbirds is of great concern. Here, we compare the changes in waterbird populations before and after habitat alterations in Caisang Lake and assess the driving factors leading to the dramatic changes in waterbird populations. Results indicate that wintering waterbird populations were significantly impacted by altered forage availability, with species-and guild-specific responses. Dramatic habitat alterations from planting lotus caused significant declines in areas of native vegetation, mudflats, and water that may have caused associated declines in herbivores, insectivores, and fish-eating waterbirds, respectively. In contrast, the increased size of the lotus area appears to have led to an increase in omnivorous waterbirds. A food shortage, potentially caused by a large area of Caisang Lake being used for culturing crab, might be another cause of the observed decline in fish-eating waterbirds. This study demonstrates a powerful approach to systematically evaluate waterbird responses to wetland management policies. These findings are important as efforts are made to protect the wintering waterbirds from the effects of human intervention, particularly at other Ramsar wetlands.