<p>Birds are very sensitive to habitat change, making them a good indicator of biodiversity response to habitat modifications. Changing any component of the ecosystem will affect the associated species diversity negatively or positively. Plant cover, especially reeds (<i>Phragmites australis</i>), shapes the topography of Lake Manzala, northern Egypt, plays an important role in water cleaning, and is a crucial resource for wintering migratory waterbirds. The complete transformation of Lake Manzala due to the dredging process that aimed to restore the lake from brackish to its original saline nature through a broader connection to the sea led to a decline in reed plants. As Lake Manzala is one of Egypt’s important bird areas (IBA), and the main stopover for migratory birds that winter in it, this study aimed to assess the difference in waterbird community composition and diversity before and after dredging and give a clear picture of the current situation of one of the main IBAs in Egypt. The study compares the situation before the removal of reeds in the winter season of 2018 and after their removal in the winter season of 2021. The results showed a decline in the overall diversity of waterbirds after dredging. The dredging process resulted in an increase in Pelecaniformes and Anseriformes abundance, a decrease in the abundance of the two orders that mainly structure the waterbird community: The Charadriiformes and Ciconiiformes, and the disappearance of order Gruiformes and the two families Charadriidae (plovers’ family) and Scolopacidae (sandpipers’ family) of Charadriiformes order. Analysis of biplot ordinations showed that waterbird diversity is associated with vegetation cover. The present data demonstrates that the removal of plant cover negatively affected the suitability of Lake Manzala for different bird communities. It also suggests that recolonization of reeds as an important ecosystem component for migrant birds can help in habitat restoration and biodiversity protection.</p>