The Ministry of Agriculture, Forestry and Fisheries reclaimed Isahaya Bay to promote agriculture and prevent natural disaster, such as a storm surge. As part of surveys being conducted to monitor the environmental impact of this reclamation project we recorded bird species observed in Isahaya Bay and counted the number of individuals belonging to some orders, such as waterfowl and shorebirds. We divided the whole study period into three, based on the establishment of a sea levee and the completion of the project, and then compiled the change of avifauna corresponding to those periods. Before the reclamation project, Isahaya Bay was a major habitat for the birds living in tidal flats that represented the shorebirds. The establishment of the sea levee resulted in disappearance of the tidal flat; consequently, Pluvialis squatarola, Numenius qrauata, N. madagascariensis, Calidris alpina, Tadorna tadorna, Larus saundersi decreased in number. The project also established a regulating reservoir; thereafter, Anas strepera, A. falcata, A. penelope, Aythya marila, A. ferina, A. fuligula, Podiceps cristatus, Fulica atra increased in number. It is noteworthy that since 1997 when reclaimed land was created, the following endangered birds were regularly observed: the genera Anser (including A. fabalis and A. albifrons) and Grus (including Grus vipio and G. monacha), Circus spilonotus, Glareola maldivarum, Sterna albifrons and Falco peregrinus. As a shrub community including Mallotus japonicus, Ulmus davidiana and Celtis sinensis grew in the Phragmites australis community, the following species that inhabit the forest landscape increased in number; Aegithalos caudatus, Troglodytes troglodytes, Poecile varius, Eophona personata.