Considered the eastern most national wildlife refuge of the Mississippi Flyway, Wheeler NWR supports Alabama's largest concentration of wintering waterfowl. It has supported up to 60,000 geese and near 125,000 ducks, although modern peaks until 1990 were nearer 30,000 geese and 75,000 ducks. Since 1990, winter goose populations have dropped significantly; below 15,000 from 1990-1995, near 5000 from 1995-1999; and near 2000 since 1999. Snow Geese are now the most prominent component of the winter goose population, peaking near 2,500.
Wintering duck species common at Wheeler NWR include wood duck, gadwall, American wigeon, American black duck, mallard, northern shoveler, northern pintail, green-winged teal, canvasback, ring-necked duck, lesser scaup, bufflehead, and hooded merganser. Mallards are the most abundant wintering species, followed variously by gadwall, green-wing teal, northern pintail, northern shoveler, lesser scaup, and hooded merganser.
Resident wood ducks are common with breeding/production probably being limited by natural cavities and quality brood habitat. Early in the 20th century, nesting cavities for wood ducks became scarce. Many landowners, including Wheeler National Wildlife Refuge, began placing nest boxes in appropriate habitat. Today, the refuge maintains about 226 boxes. These are checked at least once each year to determine how many were used and the amount of reproduction that occurred. Eggs that have not hatched and shells of those that have can be counted to give us an idea of the success these boxes are having on the local wood duck population. The Refuge also conducts pre-season wood duck banding.
Traditionally, duck numbers peak during the first two weeks of January. During the October 2005- March 2006 survey season, the highest number of ducks occurred in early January 2006 at 56,655. After November 1, all duck numbers were higher in the 2005 -2006 season than during the 2004 – 2005 season.
Currently, the most numerous goose species present are snow geese, Canada geese, and white-fronted geese, respectively. Snow goose numbers are increasing, but have begun to stabilize in the past few years. The highest number observed in 2005 – 2006 waterfowl season was 1,900, which is a slight drop from the 2,400 observed in the 2004 – 2005 season.
The highest one-day number of Canada Geese recorded in the 2005 – 2006 season was 1,360, which is lower than the 1,975 number recorded in 2004 - 2005. Both are a decline from the high number of Canada Geese observed from the previous five years (1998-2002), which has been between 2,000 and 4,000 birds. This is also a decline from the numbers counted from 1993-1997, which were between 2,900 and 23,000. The decreasing trend of Canada Geese using Wheeler NWR continues.
In contrast to Canada geese, sandhill crane numbers are increasing at Wheeler NWR. Prior to 1997, sandhill cranes occurred in small numbers on the Refuge. In 1997, 26 were observed and by 2002 the number wintering on the Refuge had increased to almost 400. In 2005-2006 a record of 1,140 sandhill cranes were documented by Refuge staff. The number continues to increase each year. In 2009-2010, there were over 8,000 sandhill cranes wintering on the refuge.
Birds generally use the fields on Mooresville and Beaverdam Peninsulas, Penny Bottoms, and on Flint Creek Island, and roost in the shallow water areas of Limestone Bay and Flint Creek.