Understanding and predicting animal distribution is one of the most elementary objectives in ecology and conservation biology. Various environmental factors, such as habitat area, habitat quality, and climatic factors, play important roles in shaping animal distribution. However, the mechanism underlying animal distribution remains unclear. Using generalized additive mixed models, we analyzed the effects of environmental factors and years on the population of five Anatidae species: Tundra swan, swan goose, bean goose, greater and lesser white-fronted goose, across their wintering grounds along the Middle and Lower Yangtze River floodplain (MLYRF) during 2001-2016. We found that: (1) All populations decreased except for that of the bean goose. (2) The patch area was not included in any of the best models. (3) NDVI was the most important factor in determining the abundance of grazing geese. (4) Climatic factors had no significant effect on the species in question. Our results suggest that, when compared to habitat area, habitat quality is better in predicting Anatidae distribution on the basin scale. Thus, to better conserve wintering Anatidae, we should keep a sufficiently large area at the single lake, as well as high quality habitat over the whole basin. This might be achieved by developing a more strategic water plan for the MLYRF.