Wetlands are crucial habitats for both migrant and resident bird assemblages. The distribution and habitat preferences of birds in aquatic ecosystems are significantly influenced by environmental and ecological factors that critically impact the relevant habitats. In order to reveal the distribution and habitat preferences of the birds, many statistical models and methodologies are employed in ecology and conservation biology. Herein, we investigated the effects of year, season, habitat, and species variables on the distribution and population dynamics of waterfowls and shorebirds associated with the wetland. In this regard, field surveys were carried out in and around Çıldır Lake (Ardahan, Türkiye) between April 2017 and September 2018 to examine the distribution of waterfowls and shorebirds and variations in population sizes. As an experimental design, a stratified random sampling design was used to assess bird fauna in the four dominant habitat types (open water surface, reeds, grasslands, and agricultural areas) in the study area. Accordingly, a total of 51 waterfowl and shorebird species were identified during the study period. Of the identified families, Anatidae (n = 18), Scolopacidae (n = 8), and Ardeidae (n = 8) were the most common families. Considering bird species, common coot Fulica atra and mallard Anas platyrhynchos were the most abundant species. The dependent variable (bird populations) was compared with the independent variables (year, season, habitat, and species). The population in 2018 decreased by 13% in comparison to the population in 2017 (p < 0.05). Once the reed area was considered as the reference, the population density in the water surface habitat increased by 65% (p < 0.001). In relation to seasonal reference, a 65% increase in population growth in spring was recorded in comparison to the growth in fall (p < 0.001). On the other hand, no statistical differences were noted in population growth in winter and summer ((p > 0.05). With respect to the reference species (Anas crecca), critical differences in species fluctuation were observed among species (p < 0.001). Consequently, the findings of the present study suggest that seasonal factor might be of the substantial factors linked to the habitat composition. However, more descriptive and predictive analytical methods are needed beyond classical regression approaches in habitat use and selection studies at bird ecology.