Refuge staff at Squaw Creek National Wildlife Refuge manage habitat to benefit wildlife. Refuge managers change water levels and mow and disk fields to benefit migrating waterfowl and shorebirds in the spring and fall and nesting marsh and water birds in the summer.Moist soil plants such as smartweed, rice cutgrass, and wild millet grow during the summer months and then marsh units are flooded in the fall where waterfowl feed on the moist soil plant seeds.Refuge personnel conduct prescribed burns to prevent invasive and woody plant growth. The tallgrass prairies consisting of big bluestem, little bluestem, Indian grass, and switchgrass have nearly vanished in the Midwest. Refuge staff members have restored some native prairie on the Loess Hills and in the wetlands.
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Bald eagles migrate to the refuge by late fall and early winter. As many as 300 immature and adult bald eagles and an occasional golden eagle may be seen during the migration peak, usually by the first of December. A record 476 bald eagles were counted during a 2001 survey. The first recorded successful bald eagle nest fledged three young eaglets in the summer of 1997. A few bald eagles may spend the winter and summer on the refuge. Migrating eagles leave the refuge in spring and summer returning to lakes and streams in the northern forests.