Nassau River - St. Johns River Marshes and Fort Clinch Aquatic Preserves are in the northeastern part of the state along the Atlantic intracoastal waters of the St. Marys, St. Johns and Nassau Rivers.

The Nassau River - St. Johns River Marshes Aquatic Preserve, located in Nassau and Duval counties, was designated an aquatic preserve on November 24, 1969 to protect the Nassau Sound area marshes and associated waters. This area consists of a vast saltmarsh estuary with numerous interconnecting tidal creeks, rivers and channels with some small tree islands. The preserve is approximately 69,000 acres.

Fort Clinch State Park Aquatic Preserve (also called Fort Clinch Aquatic Preserve), in northeastern Nassau County along Amelia Island, was designated on March 4, 1970 to provide an aesthetic buffer for the state park and historic Fort Clinch. The preserve surrounds the state park and is largely comprised of open waters around St. Marys Inlet, the Amelia River and a three mile extension into the Atlantic Ocean off Amelia Island. The western edge of the preserve borders extensive saltmarsh along Amelia Island and the preserve extends to the Florida-Georgia border. This preserve is about 7,600 acres.