This work aims to study the diverse migrating waterbirds in the New Valley area at the natural lakes in Dakhla, Mut and at the artificial agricultural wastewater in Kharga during the period from December 2022 to April 2023. This study focused on the winter and spring migration seasons and 32 different bird species were recorded, of which 29 were migratory. The observed birds belong to 8 different orders and 12 families. The largest group was the Charadriiformes order with 14 bird species. Also, Near Threatened Ferruginous Duck was recorded in Dakhla and relative abundance analysis spotlighted two key species the little stint and marsh sandpiper. The results shed light on the ecological importance of shallow water zones comparison to deep water zones, which had 84.4% from total recorded birds. Dakhla is characterized by higher overall abundances, richer species numbers, and a more diverse Shannon-Weiner index, 2.611 pointing to a more varied and populous avian community compared to Kharga. While Dakhla boasted greater diversity indices, the measurements from both sites similarly suggested that the bird species were evenly spread throughout each location. Both locations exhibited substantial increases in the diversity and populations of species, underscoring the valuable role of agricultural wastewater habitats as resting habitats of migrating waterbirds.