Big Oaks National Wildlife Refuge hosts one of the world’s largest populations of Henslow’s sparrows with over 500 pairs on the refuge. These migratory birds can be found singing in the larger grasslands during the spring and summer breeding season. The best opportunity to see Henslow’s sparrows is through a guided bird tour. It is recommended that visitors call ahead to arrange a birding tour.
 

Cerulean warblers are found nesting high in the forest canopy at the north end of Big Oaks Refuge. They are found at the refuge during the spring and throughout the summer. Visitors to the refuge may have the opportunity to see a cerulean warbler in the day use area. Listen for the male's song, and be ready to strain your neck! Binoculars recommended.
 

State endangered river otters were reestablished at the refuge in the 1990’s . They have been quite successful at the refuge and may be spotted any time of the year. The refuge contains more than 6,000 acres of wetland habitat, including Old Timbers Lake. The otters have also taken advantage of the many beaver impoundments scattered throughout the refuge.
 

Grasslands were once common in Indiana and now are rare habitats; these habitats provide shelter, breeding sites, and food for many rare plant and animal species that are only found at Big Oaks Refuge, such as Henslow's sparrow and Kirtland's snake. Big Oaks Refuge also contains the largest concentration of crawfish frogs in the state, which depend on the grassland habitat.

 

Big Oaks Refuge contains at least 32 caves. The caves, seeps and springs on the refuge are unique for their invertebrate fauna. Some invertebrate species new to science were described in these caves. Other vertebrate species, such as salamanders and bats, use some of these caves during certain times of the year. However, despite the fact that Big Oaks National Wildlife Refuge has large numbers of bats within forested areas of the refuge during the summer, the caves on the refuge do not contain significant numbers of hibernating bats. This is likely due to the small size of the caves and to inadequate temperatures and humidity within the caves. All refuge caves are closed to the public.

Wet, flat forest communities known as flatwoods are common on the refuge and contain several rare species, including the four-toed salamander and the locally endemic streamside salamander. Clay layers in the soil cause these woods to be wet in the winter and spring, but these forests can be very dry in the summer and early fall. They have acidic soils where wet races of American beech, swamp chestnut oak, sweet gum, and tulip tree fill the canopy.