The Mississippi River is a significant bird migration route. It is estimated that 40% of the nations waterfowl and shorebirds use the river valley during spring and fall migration. Daily high waterfowl counts in the fall of 2005 exceeded 600,000 birds in pools 4 thru 9.
Fall concentrations of Canvasbacks represent up to 50% of the continental population, and Tundra swans are estimated at 20% of the eastern North American population, with daily totals of more than 20,000 in pools 4 thru 9. Diving ducks gather in the open water, while the puddle ducks are found in the shallow backwaters.
Fifteen to twenty waterbird nesting colonies are found on the refuge containing more than 5,000 nests. On pools 4 thru 8 the number of nesting Great blue herons ranged from 786 - 1,306 pairs between 1999 - 2002.
The Mississippi River is the most important Bald eagle wintering area in North America. Bald eagle wintering numbers on this IBA vary within years depending on weather and ice cover. Mid-winter counts ranged from 321 in 2004 to 58 in 2005 between Winona and LaCrescent. Winter eagle roosts are located at Read's Landing and Whitman Dam.