Wetlands are vital ecosystems for waterbirds, are experiencing global decline due to human activities. Our study investigated the population dynamics and habitat preferences of waterbirds in six geographically distinct wetlands (Chashma, Dhap Chapak, Taunsa, Haleji, Raja, and Uchali) along the Indus River flyway. Point count methods were used during five consecutive migratory seasons (September and March from 2017 to 2022). In total, 73 waterbird species from 19 families and 11 orders were detected. Species richness varied significantly (F5, 437 = 8.14, p < 0.000) across wetlands. we recorded species richness (R = 73.0), species diversity (H' = 3.714), population trend (λ = 0.031), and species dispersion (E = 0.865). Chashma wetland exhibited the highest species richness (S = 52), relative abundance, and diversity. Uchali had the highest population of waterbirds (26.612%), while Raja displayed the uniform species dispersion (4.184%). Two globally endangered Pallas fish eagle (Haliaeetus leucoryphus) and Black-bellied tern (Sterna acuticauda) and seven Near Threatened water bird species: Black-tailed godwit (Limosa limosa), Great painted snipe (Rostratula benghalensis), Oriental darter (Anhinga melanogaster), Northern lapwing (Vanellus vanellus), Indian river tern (Sterna aurantia), Asian Woolly-necked stork (Ciconia episcopus), and Lesser flamingo (Phoeniconaias minor),were detected, highlighting the significance of these wetlands for conservation.We recommend regular monitoring by wildlife authorities to track population trends, assess habitat suitability, and identify threats. Conservation efforts should prioritize water regime maintenance, pollution control, and community engagement for long-term wetland management and waterbird conservation.