An array of waterbird species use the Saginaw Bay Area as a migratory stopover site, wintering ground, and breeding ground. Large migratory congregations of the columbianus subspecies of Tundra Swans (as many as 12,220 individuals) have been counted in November. Other significant migrant waterfowl concentrations include 505 American Black Ducks (Nov. 2003), 1550 Mallards (Nov. 2003), 9125 Redheads (Nov. 2004), 1748 Common Goldeneyes (Nov. 2002). Merganser spp. counts as high as 25,150 and 15,570 and Scaup spp. counts of 21,570 and 22,710 have also been made.

Several important waterbird breeding colonies also exist within this IBA, including the Contained Disposal Facility (CDF) offshore of Bay City which supported the following numbers of nests during 1997-1999: 234 Common Tern, 324 Caspian Tern, 28,605 Ring-billed Gull, 243 Great Egret, and 480 Black-crowned Night-Heron.