The National Estuarine Research Reserve System (NERRS) is a nation-wide network of state owned and managed coastal protected areas. These are designated and supported by the National Oceanic and Atmospheric Administration (NOAA) under the United States Department of Commerce.

The sites represent the diverse estuarine and estuarine-like systems of America's coasts, setting them aside for long-term research and management based on biogeographic regions. The mission of the Reserves is to promote informed management through linked programs of stewardship, public education, and scientific understanding.

The New Hampshire Fish and Game Department under the Marine Fisheries Division manages the Great Bay NERR. Designated in 1989, the Reserve's primary purpose is to promote the wise use and management of the Great Bay Estuary. Encompassing over 25,000 acres of tidal waters and uplands, the Reserve is part of the Atlantic flyway and located in the Arcadian bioregion.