Hydro-meteorological factors substantially influence the capacity of aquatic ecosystems to support migratory water-roaming birds. In the context of climate change, understanding the impact of the shifting weather patterns and water availability on the suitability of migratory waterbird habitats is crucial for effective conservation and management strategies. Species Distribution Models (SDMs) are proficient tools for assessing the impact of environmental variables on habitats and distribution of species living in those habitats. In this study, we aim to determine the link between hydro-meteorological dynamics and sustaining migratory waterbird habitats in Rajshahi, Bangladesh, using Maximum Entropy (Maxent) modeling. Changes have been observed in eight selected hydro-meteorological variables: Humidity, evapotranspiration, soil moisture, rainfall, land surface temperature, air temperature, vegetation, and water body extent throughout three time steps: winter 2022 (October 2022 to January 2023), spring 2023 (February to April 2023) and winter 2023 (October to December 2023). Variations in the abundance of migratory waterbirds belonging to four orders such as Anseriformes, Charadriiformes, Pelecaniformes and Podicipediformes have also been observed during the same time periods. Maxent model was used to (1) analyze the significance of each hydro-meteorological variable individually in the targeted water-roaming bird habitats and (2) predict the highly probable areas of presence for each order and determine the changes in the orders’ probable suitable habitat with changes in the hydro-meteorological variables. Analysis of hydro-meteorological variables reveals considerable fluctuations among the three time steps. Results obtained during the model run indicate hydro-meteorological variables have dissimilar impacts on aquatic habitats depending on the seasons and environmental settings. The AUC (area under receiver operating characteristic curve) values were also greater than 0.8, which entails the model’s superior skill in linking hydro-meteorological information to water-roaming bird habitat suitability. In addition, significant changes in the predicted area of suitable habitat were observed between the time steps. The highest reduction occurred for the order Podicipediformes, where the total predicted area of presence reduced from 222.44 hectares in winter 2022 to 55.78 hectares in spring 2023. Comparing between winter 2022 and winter 2023, the area for the order Anseriformes was subject to the maximum downtrend, declining from 110.63 hectares (winter 2022) to 68.98 hectares (winter 2023). Anomaly in the climatic and hydrological patterns can therefore significantly deteriorate the suitability of water-roaming bird habitats. This study confirms the urgency to increase conservation concerns taking hydro-meteorological perspective into consideration.