Over 500 pairs of the State-endangered Henslow's sparrow are estimated to breed in the large grasslands of Big Oaks. The refuge has been designated as a "Globally Important Bird Area" because of its value to Henslow's sparrows and other migratory birds. Federally-threatened bald eagles and osprey are also known to use the refuge as a migratory stopover or wintering site.

Wetland habitat areas (over 6,000 acres) are popular areas to view wildlife. These areas include the 165-acre Old Timbers Lake, an employee volunteer project constructed in the early 1970s. New beaver impoundments are naturally increasing the number and diversity of wetlands found on the refuge. Wetlands are attractive to a wide variety of wildlife, including river otters, beavers, wading birds, wood ducks, and other waterfowl. A great blue heron nesting colony found on the refuge supports over 50 nests in the spring.

Large blocks of forested habitat can also be found at the refuge. Extensive forests are rare in Indiana, and many species of wildlife that require them benefit from their conservation and management. Several wildlife species can be seen in these areas, including wild turkey, cerulean warblers, wood thrushes, worm-eating warblers, and other neotropical migratory songbirds.

Young forests and shrublands are scattered throughout the refuge and provide habitat for many plant and animal species. Prairie warblers, yellow-breasted chats, and American woodcocks make their homes in these areas.

The vast grasslands on the refuge provide high-quality habitat for many species of grassland-dependent birds. A variety of songbirds use these areas, including one of the world's largest populations of Henslow's sparrows. Red-tailed hawks and northern harriers may be viewed foraging over the grasslands in search of food. White-tailed deer, bobwhite, fox squirrels, coyotes, cottontails, raccoons, and opossums are frequently observed along grasslands, woodland and road edges, and fields.