The Whitewater Valleys IBA covers over 46,000 acres and is an ecological gem in southeastern Minnesota. The area is made up of bluffs and valleys containing numerous spring-fed creeks, streams and rivers. This multiplicity of habitats provides for a wide diversity of bird-life. Approximately 250 species use the valley for migration and breeding including 25 species of waterfowl, 22 species of shorebirds, 31 species of warblers and 17 species of sparrows. Over 100 species are potential breeders in the area. Sandhill Cranes (at least three pairs) and Bald Eagles (two nests) nest within the area. Up to 100 Bald Eagles use the valley as a migration stop-over site or a winter roost site. Surrounded by agricultural lands, the size and quality of the habitats within this IBA, and the birds they support, are rare in southeastern Minnesota.

The Whitewater Valley, a tributary river valley of the Mississippi River, is located in Winona County in southeastern Minnesota approximately 25 miles east of Rochester. Minnesota Highway 74 provides the best access running north to south through the valley for ~ 20 miles. The south end of the valley where Whitewater State Park is located is 8 miles north of St. Charles, MN on Highway 74. The north end of the valley is located at the junction of US Highway 61 and Highway 74 at the town of Weaver, MN 20 miles north of Winona, MN.

Contained within the IBA are the South, Middle and North Branches of the Whitewater River, Beaver and Logan Creeks and the Dorer Pools which are part of the Whitewater WMA. Whitewater and Carey State Parks are included within this IBA. The area contains many types of habitat including up land and lowland deciduous forests with a mixture of white pine, jack pine and cedar, oak savanna, marsh and other wetland complexes and bluff prairies. The diversity of bird species using this area makes it a very strategic IBA in the State of Minnesota.

With the close proximity of the Mississippi River migration corridor to the Whitewater valleys, this area is an excellent stop-over region for migrant birds during both spring and fall. A total of 242 species occur within the boundaries of the IBA. Species of conservation concern recorded with the Whitewater Valleys IBA are: Bald Eagle (r), Red-shouldered Hawk (b), Cerulean Warbler (b), Acadian Flycatcher (b), Louisiana Waterthrush (b), Peregrine Falcon (m), American Woodcock (m)Black-billed Cuckoo (m/r), Whip-poor-will (m/r), Red-headed Woodpecker (m/r), Wood Thrush (m/r), Golden-winged Warbler (m), Prothonotary Warbler (m/r), Canada Warbler (m), Bobolink (m/r). These Floodplain forest species are found in this IBA as well: Red-shouldered Hawk, Black-billed Cuckoo, Yellow-billed Cuckoo, Barred Owl, Yellow-bellied Sapsucker, Pileated Woodpecker, Eastern Wood-Pewee, Acadian Flycatcher, Least Flycatcher, Great Crested Flycatcher, Yellow-throated Vireo, White-breasted Nuthatch, Brown Creeper, Blue-gray Gnatcatcher, Veery, Golden-winged Warbler, Blue-winged Warbler, Cerulean Warbler, American Redstart, Prothonotary Warbler, Louisiana Waterthrush, Scarlet Tanager. These Upland Deciduous Forest are found in the IBA: Red-shouldered Hawk, Broad-winged Hawk, Ruffed Grouse, Black-billed Cuckoo, Yellow-billed Cuckoo, Barred Owl, Whip-poor-will, Yellow-bellied Sapsucker, Pileated Woodpecker, Eastern Wood-Pewee, Acadian Flycatcher, Least Flycatcher, Great Crested Flycatcher, Yellow-throated Vireo, White-breasted Nuthatch, Blue-gray Gnatcatcher, Veery, Wood Thrush, Blue-winged Warbler, Chestnut-sided Warbler, Cerulean Warbler, American Redstart, Ovenbird, Louisiana Waterthrush, Scarlet Tanager.

These species occur sporadically or as migrants: Tufted Titmouse (sporadic), Brown Creeper (m), Golden-winged Warbler (m), Black-throated Blue Warbler (m/sporadic), Mourning Warbler (m), Worm-eating Warbler (m/sporadic), Kentucky Warbler (m/sporadic), Hooded Warbler (m/sporadic).