Refuge lands are managed for migrating waterfowl.  The wood duck is one species that breeds in the Minnesota River Valley.  The floodplain forest habitats in the refuge provide an ideal home for wood ducks.  They are cavity nesters, preferring abandoned holes in cottonwoods, maples, oaks, and ash trees.  Wood ducks typically choose a tree 2 feet in diameter, with a cavity anywhere from 6 to 60 feet high.

River otters thrive on the refuge where there is high quality water and abundant food supply.  River otters settle in areas with significant coverage, usually vegetation or physical structures such as rock piles.  They do not dig their own homes,instead they use naturally occurring shelters or abandoned burrows and dens.

The prairie skink is the only lizard found on the refuge.  Restoration of prairie and oak savannas on the refuge has created high quality habitat for this sandy soil burrower.  Look for them basking on top of rocks or logs and actively foraging for crickets, grasshoppers and spiders.

Floodplain forests historically dominated much of the floodplain along the Minnesota River.  Today, this plant community continues to provide migration and nesting habitat for several significant birds that are a priority for the U.S. Fish and Wildlife Service.  These include the red-headed woodpecker, red-shouldered hawk and wood duck.  Minnesota Valley National Wildlife Refuge monitors and restores the forest community to include cottonwood, sliver maple, American elm, green ash, and wood nettle.  Several floodplain forest areas on the refuge are closed to protect bald eagle nests and heron and egret nesting colonies from human disturbance throughout the breeding season.  Make sure to observe posted closed areas.

The refuge is reestablishing native prairie grasses and wildflowers that once dominated the prairies and oak savanna through active vegetation removal, planting, and prescribed fire.  After removing unwanted plants, primarily trees that are not oaks, the area is burned multiple times over several years to stimulate the growth of native grasses and forbs.  It may take more than 20 years for the full complement of native plant species to recover.  Years of fire suppression and grazing have allowed many invasive species to take over the landscape.

Refuge units contain a variety of wetlands, ranging from shallow wet meadows and calcareous fens to permanently flooded, mixed vegetation marshes.  Nearly all of the wetlands are spring-fed, and most of the larger wetlands are surrounded by mature cottonwoods, willow, silver maple, and box elder.  Water control structures have been installed on many of the refuge's wetlands, and refuge staff are able to manipulate water levels to improve the health and productivity of these aquatic communities.