Wood ducks are one species of waterfowl that finds excellent nesting habitat at Muscatatuck National Wildlife Refuge. Males usually arrive in February to check out suitable nesting cavities in forested wetland areas. Females arrive soon after the males, and egg laying occurs in tree cavities in March and April. By early May the young wood ducks hatch and leave the trees to spend the rest of the summer in refuge wetlands. In late fall, wood ducks leave the refuge and migrate south. Early mornings in mid-summer are good times to observe young wood ducks feeding in marsh areas along the auto tour route.
 

A pair of bald eagles has been nesting at Muscatatuck National Wildlife Refuge for more than a decade in an inaccessible swamp area. Between two and three youngsters have fledged each year, although the nest has blown down many times and had to be rebuilt. Both adult and immature eagles can sometimes be spotted on the refuge hunting for fish over marshes, moist soil units, and lakes.

Muscatatuck National Wildlife Refuge is also home to river otters, once common in Indiana. Their numbers dropped off because of over-trapping and loss of wetland habitat. Muscatatuck became the first otter reintroduction site in Indiana in 1995. Good viewing areas for otters are the marshes and creeks along the auto tour route along with Stanfield and Richart Lakes.

Muscatatuck National Wildlife Refuge is a pocket of wetland habitat surrounded by farmland and development. While 86% of the historic wetland habitat in Indiana was drained, many refuge wetlands survived. Refuge staff manage water levels in moist soil units, marshes, and two lakes.

Some marshes are flooded and periodically drained to encourage plant development. Moist soil units and marshes are sometimes disked to prevent trees and other unwanted vegetation from taking over. Natural springs have combined with creek drainages in the Moss Lake area to create a swamp that serves as an important sanctuary for many species of wildlife.

About 70% of Muscatatuck National Wildlife Refuge is covered by forest. Most forest at the refuge is bottomland hardwood forest that is frequently covered with water. Beaver dams are removed periodically to keep bottomland forests healthy, and trees are planted in certain areas to reduce forest fragmentation and provide diverse habitat for wildlife. The restoration of bottomland hardwood habitat is a major goal of the Big Rivers Ecosystem of which Muscatatuck National Wildlife Refuge is a part.

Areas of grassland habitat on Muscatatuck National Wildlife Refuge are periodically mowed or burned to prevent trees from taking over and to provide for many wildlife species. Grassland areas along the auto tour route provide excellent wildlife viewing opportunities for birds including meadowlarks, grasshopper sparrows, sedge wrens, and sometimes even sandhill cranes.