Located on the New Hampshire and Maine border, Great Bay estuary is a complex embayment and New Hampshire's largest estuarine system. The Great Bay Reserve offers a diversity of land and water area, including upland forest, salt marsh, mudflats, tidal creeks, rocky intertidal, eelgrass beds, channel bottom/subtidal and upland field habitats. The reserve encompasses 10,235 acres, including approximately 7,300 acres of open water and wetlands. The Bay's cultural heritage is equally diverse, from paleo-Indian villages 6,000 years ago to colonial transportation and industrial use and ultimately protection in the face of a proposed oil refinery in 1973.

The reserve is located 10 miles inland from the coast of New Hampshire and the Maine border.