Emiquon National Wildlife Refuge was established December 29, 1993 with the purchase of its first 284 acres. About 2,200 acres have been acquired to date. The refuge is being assembled to protect, restore, and manage migratory bird, fish, and resident wildlife habitat in the Illinois River Valley, while providing for increased public recreation and educational opportunities. When complete, it will contain 11,122 acres. Historically, two backwater lakes, Thompson (1,800 acres) and Flag (1,000 acres), provided excellent habitat for migratory birds, fish, and resident wildlife. The Fulton and Mason County area's ability to support an abundance of fish and wildlife and the popularity of traditional outdoor activities once made the area the tourism capital of Illinois. When restored, Emiquon will provide quality backwater lake, bottomland forest, upland forest, prairie, seasonal wetland, and marsh habitat for migratory birds, fish, and resident wildlife. An additional 1,100 acres will be retained for agricultural crops for wildlife. Emiquon Refuge is part of the Illinois River National Wildlife Refuge Complex, with headquarters at Chautauqua Refuge, in Havana, Illinois.

Emiquon Refuge is located at the confluence of the Spoon and Illinois rivers in Fulton County, Illinois. Situated just west of Havana, Illinois, on Route 97/78, the refuge is accessible by State Highway 24 from Peoria or Lewistown, and State Highway 136 from Havana, Illinois.