Lakes and wetlands provide top-priority hotspots that play a key role in maintaining and protecting threatened and migratory waterfowl. Identifying seasonal and spatial variations in aquatic bird communities and their responses to environmental factors is vital conservation efforts. However, there is a lack of information on waterfowl in Mongolian lakes and their associated wetlands. The purpose of this study was to investigate the spatial–seasonal changes in waterfowl assemblage structures in Mongolian lakes, as well as to determine how they respond to various environmental factors (lake surface area, elevation, and geographical distribution). Statistical analyses were performed using seasonal data (May, July, and September) for 28 waterfowl collected from 54 lakes across the country between 2016 and 2018. Seasonal heterogeneity in species richness and abundance was observed in lakes in each geographical region (Eastern, Central, and Western Mongolia). The composition of waterfowl in the lake was also relatively similar between May and September compared to July. This was due to the overlapping migration seasons in spring and autumn. Regionally, the number of waterfowl was much higher in the Eastern Mongolian lakes, followed by Central Mongolian lakes and then Western Mongolian lakes. This is likely due to differences in habitat availability and water levels between the regions. Eastern Mongolian lakes tend to have more wetlands and shallow water habitats, while Central and Western Mongolian lakes tend to have deeper open-water habitats. These differences in habitat types could contribute to the observed differences in waterfowl abundance among the regions. Additionally, some small lakes and the group of small lakes supported a greater abundance and diversity of waterfowl compared to some medium-sized and large lakes, suggesting that they are important for conservation. Indices of diversity (H’) and species dominance (D’) showed positive and negative correlations with lake surface area, respectively. Perhaps the increased surface area of the lake decreases the habitat overlap for designated waterfowl due to habitat heterogeneity. Accordingly, the indices (H’ and EH) increased as the waterfowl species composition became relatively equivalent in large lakes. Overall, spatial variations among the lakes were primarily attributable to the individual features of the lakes (shallowness, small lake groupings, and surface area), and seasonal variation in the lakes depended majorly on the compositional changes of the waterfowl due to migration.