The study proposes to discuss about the seasonal water bird diversity, habitat preference, assemblages of water bird species and their conservation problems in different agroecosystems. Field visits was done once in a week during Jan. 2021-Jan. 2023. Freshwater and saline agroecosystems are the study areas used for the water bird survey. The water bird study was conducted by direct observation method, point count method and line transect method. Observations were made using binoculars (10 × 50 Nikon) and video camera (Nikon Coolpix p1000). Based on the pilot study in 2020, we decided to concentrate on 16 species of waterbirds coming in the 3 different orders i.e., Order Pelecaniformes, Ciconiiformes and Suliformes. Compared to the different study areas, a greater abundance of water birds was recorded in winter season, while a lesser abundance was observed in the monsoon season. The species richness was highest in saline agroecosystem and water bird congregation was more in freshwater agroecosystem. Saline agroecosystem was the most preferred habitat used for water bird species. Agroecosystems support the globally threatened water bird species such as spot billed pelican, darter, black headed ibis and painted stork. Many factors that are listed below threatens the agroecosystems and it causes the decreasing assemblages of water bird species. They are high water intake due to heavy rain, electric lines, high growth of water hyacinth, fishing nets, solid wastes and garbage deposited from toddy shops, pesticides used in fresh water rice farming, tourism, crackers, high level of fishing activities, habitat destruction, communication towers, predators and white flags were introduced by farmers.