Though the refuge is not a major shorebird stopover it does provide habitat for respectable numbers, consisting of over 25 species. The timing and duration of the moist-soil and agriculture impoundments coincides with the spring migration period of most shorebird species. During the fall when most of the impoundments are in the process of being flooded shorebird habitat is essentially limited to TVA’s annual drawdown of Kentucky Lake.
An abundance of mudflats on Kentucky Lake during TVA's drawdown provides good habitat for shorebirds during the fall migration. The late winter and spring drawdowns of refuge impoundments provide mudflats for the spring migration.
Some species that are commonly found on the refuge are the solitary sandpiper, greater yellowlegs, lesser yellowlegs, pectoral sandpiper, least sandpiper, semipalmated sandpiper, spotted sandpiper, killdeer, and semipalmated plover.
Shorebird surveys are conducted along a route in the Duck River Bottoms to assess the impacts of the management practices that occur within several impoundments. This data is collected following the International Shorebird Survey protocol and is provided to Manomet and the Tennessee River Valley Shorebird Committee. This committee was recently formed to assess the importance of shorebird habitat within the Tennessee River Valley and impacts of recent modifications TVA has made to some of the drawdowns schedules of several reservoirs in their system.
Habitat adjacent to Kentucky Lake has declined for shorebirds in the past several decades because water levels are maintained at a higher levels longer for boating and recreational interests. Research is now being conducted by the University of Tennessee to assess the value of Kentucky Lake as a shorebird stopover site during fall migration. To balance the loss of habitat adjacent to Kentucky Lake the refuge seeks to provide habitat in the managed impoundments of the Duck River Unit.
A variety of gulls and terns, such as the herring gull, ring-billed gull, Bonaparte's gull, common tern, black tern, and Caspian tern, utilize the refuge. The Big Sandy Unit of the refuge is noted for the occurrence of bird species outside of their normal range.
The Fish & Wildlife Service operates the Shorebird Sister Schools Program that encourages public participation and connects educators to the conservation of shorebirds and their habitats.