The refuge is actively conserving and restoring wetlands for the benefit of wildlife. Goals of the wetlands restoration program include providing 1,000 acres of restored wetlands, improving 150 acres of wetland habitat with new lake water level management, improving migratory habitat on 100 acres of existing wetland management units, and reducing disturbance during critical periods. 

Tallgrass prairie used to cover millions of acres in the Midwest. Today, as little as 1% of the prairie remains. Since the creation of the refuge, thousands of acres of agricultural fields at Boyer Chute National Wildlife Refuge have been returned to native grasslands. Prescribed burning is one of the tools used to maintain the restored tracts of prairie.
 

River restoration projects in cooperation with other agencies provide habitat for fish and wildlife along the Missouri River.