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The refuge is bisected by 20 miles of the famous Suwannee River and includes 30 miles of coastal marsh habitat along the Gulf.  Established on 10 April 1979, the salt marshes and tidal flats at the river's mouth are a paradise for shorebirds and fish.  The flow of the Suwannee River fuels the highly productive estuarine waters of the Gulf, providing habitat for Gulf sturgeon and feeding grounds for resident and migratory shorebirds, wading birds and waterfowl that make this place their home.  The refuge also encompasses an unusual diversity of floodplain hardwoods, cypress-lined sloughs, cabbage palm and cedar islands, cypress domes, hydric, mesic, and xeric hardwood hammocks, and low pine flatwoods.

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