Native Americans of the Abenaki and other nations have inhabited the region around Great Bay for thousands of years, sustained by its rich natural resources. The Native Americans that lived on the shores of Great Bay survived on the fish, shellfish, waterfowl and mammals that were found in abundance in and around the estuary.

The first European to explore and write about the area was English explorer Martin Pring in 1603. Pring is believed to have sailed his ship up the Piscataqua River all the way into Great Bay looking for sassafras, considered to be a plant with great medicinal value. The early 1600s brought the arrival of permanent European settlers.

The first true settlers were fishermen who landed on the Isle of Shoals in 1623. The islands became an important fishing area for the early British and French colonies. Small settlements were also established the same year at Odiorne Point (called Pannaway) in Rye and Dover Point where Edward Hilton set up his trading post. Today, Dover Point serves as the eastern boundary of the Great Bay NERR.

Portsmouth, New Hampshire’s only port, was later settled by English immigrants in 1630 and named Piscataqua after the Abenaki name for the river. It was later called Strawbery Banke for the wild strawberries growing along the riverbank. The town of Portsmouth was incorporated in 1653, named after the colony’s founder, John Mason, a ship captain from Portsmouth, England.

These early residents used the Bay to transport their harvests. The tidal influence was the perfect way to move goods without much human or animal effort. A simple, flat-bottomed boat called a Gundalow was developed to make use of the tides and carry heavy loads in shallow waters. Dried fish, furs and lumber were exported from the region in exchange for much needed supplies. The waterways of the estuary also provided access to settlements on the tributaries and the Native American tribes.

Control of the region was contested throughout the French and Indian Wars. The conflict peaked with a raid on Oyster River Plantation (now Durham) by a mixed force of French and Native American combatants, retaliating on the settlement for broken treaties, destroyed and stolen lands, and failed peace negotiations. Nearly one hundred colonists were killed or captured in the raid, and the settlement was burnt. However, the area was eventually re-colonized. 

The tidal portion of the Oyster River is included within the Reserve boundary. In 2014, archeological research was undertaken along the river in an attempt to locate the original Oyster River Plantation settlement. The results of that research have been published in several New England archeology journals and local publications. The Reserve stewards sites which may contribute to further discoveries and an improved understanding of the pre-colonial and colonial history of the area.

Gundalows transported many types of freight. Saltmarsh hay, lumber, fish, clay and textiles were just a few of the cargos. Salt hay harvested along the shores was used as food and bedding for horses and cattle. Sawmills located along the tidal rivers produced lumber that was exported through Portsmouth to other US ports. The lumber produced also fueled the shipbuilding business along the Piscataqua River and in 1800 the country’s oldest naval shipyard was established in Portsmouth (now part of Maine).

In addition to sawmills, over 40 brickyards eventually dotted the shores of Great Bay and its tributaries. The rich blue marine clay was harvested from along the estuary shores and made into bricks that were used to build locally and all around New England including some of the finest homes on Boston’s Beacon Hill.

During the late 1700s and early1800s, tidal towns such as Exeter turned from the sea to manufacturing. Exeter was home to the state’s first paper mill in 1777 and the first sailcloth factory in 1790. The first cotton factory opened in Dover in 1815 and the city became an important manufacturing hub.

In 1835, the Boston and Maine railroad made its debut in New Hampshire and essentially took the place of Gundalows. Speed and year round operation made the rails the choice for shipping cargo. By this time, most of the trees around the estuary had been cleared and the blue clay deposits largely exhausted.

Commerce Comes at a Price
The exploitation of Great Bay’s natural resources over three centuries was not without its cost. By 1750, salmon were already in decline because of the sawdust from the mills and the construction of dams that closed off their spawning grounds. In 1790, the State passed a law prohibiting the throwing of “ballast, rubbish, gravel, earth, stone, dirt, ashes and filth” into the Piscataqua River. By the 1900s, the estuary became the dirty backyard as towns began looking inward and away from the water. It quickly became a dumping ground for sewage and industrial waste. During World War II, the Portsmouth Naval Shipyard specialized in the construction of submarines and kinds of waste were dumped into the river. This practice did not end until 1976.

The Pease Air Force Base, which was located on Great Bay and operated from 1951 to 1991, also dumped hazardous materials on site. Many of these contaminants eventually found their way into Great Bay and remain in the sediments.

The largest threat to Great Bay came in the fall of 1973 when Aristotle Onassis proposed to build the world’s largest oil refinery on Durham Point. The citizens of Durham rallied against the project and it was eventually defeated in 1974. This close call set in motion efforts to protect Great Bay from future development and led to Great Bay being designated a National Estuarine Research Reserve in 1989. Today, Great Bay is enjoyed for the recreation, education and research opportunities it offers.

Great Bay is a place where the ocean and rivers, land and water, and people and nature meet. It lies at the confluence of tidally driven salt water from the Gulf of Maine and fresh water from the Salmon Falls, Cocheco, Bellamy, Oyster, Lamprey, Squamscott, and Winnicut rivers. Before reaching the bay, seawater travels 15 miles inland—a geographic configuration makes Great Bay one of the nation’s most recessed estuaries. It is often referred to as New Hampshire’s “hidden coast.”

The Great Bay estuary was formed by the melting of the glaciers more than 14,000 years ago. The rising ocean waters flooded the land and filled the river valleys that make up the bay today. Its habitats are extraordinarily diverse: eelgrass meadows, mudflats, salt marsh, channel bottom, and rocky intertidal places that are home to hundreds of bird, fish and plant species, including 23 that are considered threatened or endangered. The rivers that flow into this estuary drain a watershed that extends more than 1,000 square miles. The large quantities of water that move in and out of the estuary create some of the strongest tidal currents in North America. This tidal exchange affects water quality, habitats, and the distribution of species.

Eelgrass is a critical habitat that has many functions in the estuarine system. Eelgrass beds provide food for waterfowl, habitat for fish and invertebrates, and roots to stabilize bottom sediments. Eelgrass also maintains water quality by filtering the water allowing sediments to settle and then using the excess nutrients for growth.

At low tide, more than half of Great Bay is exposed as mudflats. Worms, soft-shelled clams, mud snails, horseshoe crabs, wading birds and many other animals rely on the flats for food, reproduction, and protection from predators. The channel bottom is a passage for fish and invertebrates at low tide and the preferred habitat for oysters. Because oysters filter the water to feed, they also help to remove pollutants and nutrients.

Expansive meadow marshes and narrow fringing marshes provide important breeding, refuge, and forage habitats for invertebrates, fish, and birds. As organisms move between salt marshes and other estuarine habitats, they help export energy to support the complex coastal food web.