Great Bay National Estuarine Research Reserve, New Hampshire

Source: NOAA


caption Great Bay Reserve boundary map. (Source: NERRS)

The Great Bay Reserve offers a diversity of land and water areas around the estuary, such as salt marshes, rocky shores, bluffs, woodlands, open fields, and riverine systems and tidal waters. It has a rich cultural history and was the first major commercial waterway developed by the early settlers.

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 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 is located in the Arcadian bioregion.

Natural Heritage

The Great Bay Estuary begins at the mouth of the Piscataqua River. Tides carry salt water into the estuary twice daily from the Atlantic Ocean. Here it mingles with the fresh water influence from the various rivers that empty into Great Bay. New Hampshire has the shortest coastline of any state, but those 18 miles increase to 150 miles of tidal shoreline when the Great Bay Estuary is included. It is one of the largest estuaries on the Atlantic Coast and at 10 miles inland is one of the most recessed.

Approximately 14,000 years ago, following the melting of the glaciers, the Great Bay Estuary was formed. The glacial melt waters contributed to rising ocean waters, which flooded the land and filled the river valleys that make up Great Bay today.

There are five very different water-dominated habitats that make up the Great Bay. In order of abundance they are: eelgrass meadows, mudflats, salt marsh, channel bottom, and rocky intertidal. These habitats are home to 162 bird, fish and plant species (23 of which are threatened or endangered), countless invertebrate species and even the occasional harbor seal.

Eelgrass is one of a very few underwater marine flowering plants. It has many functions in the estuarine system. The eelgrass community provides habitat for several organisms, especially the young of fish and invertebrates. Eelgrass roots help stabilize the bottom sediments. Eelgrass plants help maintain water quality and clarity by filtering the water allowing sediments to settle and then using the excess nutrients for growth.

More than half of Great Bay is exposed as mudflats at low tide. Worms, soft-shelled clams, mud snails, green crabs, wading birds, horseshoe crabs and many other animals utilize the extensive mudflat habitat for feeding, reproduction and protection from predators.

The channel bottom habitat provides a place for fish and invertebrates to move to at low tide. It is also the preferred habitat for oysters, a highly specialized animal that only live in estuaries.

Rocky intertidal habitat provides firm anchorage for seaweeds, barnacles, and ribbed mussels. Each winter, much of the standing crop of seaweeds becomes entrapped in ice. When the ice begins to break up in spring, the seaweeds are torn from the rocks and enter into the detrital cycle.

Regional significance

Located within the Gulf of Maine watershed, the Great Bay Estuary is a drowned river valley composed of high-energy tidal waters, deep channels and fringing mudflats. The entire estuary extends inland from the mouth of the Piscataqua River between Kittery, Maine, and New Castle, New Hampshire through Little Bay into Great Bay proper at Furber Strait, a distance of 12 miles. The Great Bay Estuary is a tidally-dominated system and is the drainage confluence of three major rivers, the Lamprey, Squamscot, and Winnicut. Four additional rivers flow into the system between Furber Strait and the open coast: the Cocheco, Salmon Falls, Bellamy, and Oyster Rivers.

The Piscataqua River is an ocean-dominated system extending from the Gulf of Maine at Portsmouth Harbor and forming the border of New Hampshire and Maine to the fork of its tributaries, the Salmon Falls and Cocheco Rivers. These rivers, several small creeks and their tributaries and ocean water from the Gulf of Maine create the Great Bay estuarine hydrosystem. The tidal range is dramatic within Great Bay. Average depth of the embayment is 2.7 meters (m) with channels extending to 17.7 m. The water surface of Great Bay covers 8.9 square miles at high tide and 4.2 square miles at low tide, leaving greater than 50% of the Bay exposed at low tide.

The Gulf of Maine is often considered by scientists and the public alike as one of the most pristine marine environments on the East Coast of the United States. As a result of its water circulation patterns and the combined productivity of its seaweed, salt marsh grasses, and phytoplankton, the Gulf of Maine is also one of the world's most productive water bodies. Historically, it has been a source of livelihood for tens of thousands of commercial fishermen. More recently, recreation- and tourism-related employment has been recognized as a major contributor to the region's economy.

Cultural Heritage

caption Boston & Maine railroad along the Squamscot river at Newfields landing, mid 1800's. (Source: NOAA)

Native Americans were the first to live on the shores of Great Bay. They survived on the abundant fish, shellfish, waterfowl and mammals that lived in and around the estuary.

The early 1600s brought the arrival of European settlers who also took advantage of the seemingly endless supply of resources. They 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, the Gundalow, was developed to make use of the tides and carry heavy loads in shallow waters.

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 to other U.S. ports. The lumber produced also fueled the shipbuilding business along the Piscataqua River until steam-powered steel vessels became cheaper to build. Brickyards also dotted the shores of Great Bay and its tributaries. 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. Cotton mills were an important part of the Industrial Revolution. Wherever gundalow ports were, mills were built.

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.

Site Description

The Great Bay Reserve is comprised of upland forest, salt marsh, mudflats, tidal creek, rocky intertidal, eelgrass beds, channel bottom/subtidal and upland field habitats.

The reserve has a diversity of habitats—Adams Point/Crommet Creek is made up of field, salt marsh, and woodlands; Lubberland Creek and Moody Point is comprised of marsh, riparian, and forested uplands; the Squamscott River Wetlands habitats include salt marsh, farmland and riparian; the Wilcox Point includes riparian and forested upland habitats; Sandy Point is wooded uplands, vernal ponds, salt marsh and mudflats.

The Great Bay Wildlife Refuge on the reserve's eastern border contains the greatest diversity of habitats, including small coves, rock promontories, woodlands, open field wetland areas and steep and shallow sloping areas.


caption (Source: NOAA)

Salt marshes in Great Bay are dominated by the Spartina alterniflora (smooth cordgrass) and S. patens (salt meadow hay). A variety of other plant species are found in Great Bay marshes. Eelgrass is distributed throughout the Great Bay Estuary. Several extensive Zostera beds occur within Great Bay. Both annual and perennial salt marsh asters are found in the reserve's brackish salt marsh areas. The region is characterized as a transition zone between the deciduous forest to the south and the coniferous forest to the north. Common tree species within the area include white pine, red oak, red pine, hemlock, red maple, quaking aspen and shagbark hickory. Uncommon southern species include black gum tree and sweet pepper bush.

Endangered Species

Two successful osprey nests are within the reserve boundaries. Common loons and pied-billed grebes forage in the Bay during migration. Common terns have nested on Nannie Island and the Footman Islands, as well as on several islands in Little Bay. Migrating Northern harriers use the salt marshes and agricultural land for foraging. Sedge wrens and Henslow's sparrows occasionally occur in short grass habitats around the bay.

Adams Point is home to robust knotweed, hairy brome grass and lined bulrush, all rare in the state. Crommet Creek has prolific knotweed, salt marsh gerardia, dwarf glasswort, four-toed salamanders and hog-nosed snakes; all rare species in the state. The Lubberland Creek/Moody Point Component has marsh elder and large salt marsh aster, both rare to the state as well.

The Squamscott River Wetlands Component boasts four rare plants: the marsh elder, the stout bulrush, the small spike-rush and the exserted knotweed. Finally, the Wilcox Point shoreline is critical to the wintering of the American bald eagle. The estuary supports the largest winter population of bald eagles in New England and is one of the best documented wintering sites for these birds in the region. Up to 19 bald eagles spend their winter months feeding on waterfowl and roosting within the reserve.

Tidal Range and River Flow

Great Bay is a mesotidal estuary with the average tidal range varying from 2.5 meters (8.2 feet) at the mouth of the estuary to 2.0 meters (6.6 feet) at Dover Point, increasing slightly to 2.1 meters (6.9 feet) at the mouth of the Squamscott River. Throughout most of the year, the tidal component of the estuary dominates over freshwater influence. The flushing time for water entering the head of the estuary is 58 tidal cycles (26.0 days) during high river flow and 48.5 cycles (25.1 days) during low river flow.

Approximately 50 percent of the average annual precipitation in the Great Bay estuary drainage basin enters the estuary as stream flow.


The region surrounding the Great Bay is included in the Seaboard Lowland section of the New England Province. The most recent glaciation of the area ended in the Wisconsin stage of the Pleistocene epoch (10,000 to 20,000 yrs. B.P.) The glaciation proceeded through the area in a southeasterly direction, resulting in the orientation of the many drumlins in the area. Substantial amounts of glacial till were deposited as the glacier receded.

Bedrock surrounding Great and Little bays is primarily metamorphic, consisting of dark gray slate of the Kittery formation visible as outcrops along the northern and western shores and in the Pierce Point area of Greenland. The Eliot formation, also dark-gray slate, can be seen along the shores of Stratham and Newington. A fold in the Eliot formation, the Great Bay syncline, passes through Newington to Thomas Point, under Great Bay, then into Stratham near Bracketts Point.

Immediately to the north and west of Great and Little bays, a granite intrusion of Exeter diorite comprising the Exeter pluton (i.e., part of the Hillsboro plutonic series) is present. Large outcrops of the slate described above serve as an important source of stable substratum for macroalgal attachment and contribute to the shingle beach common around Great Bay.

Crustal depression in New Hampshire from glacial weight was on the order of 12.2 meters (40 ft.) After glacial melt, crustal rebound occurred and is complete today. However, the uplift was not uniform throughout the region and Great and Little bays represent a sag along the surface. The low-lying area was filled by rising sea level from glacial melting. Thus, the Great Bay estuary is representative of a drowned-river valley. Present sea level was reached approximately 3,000 to 5,000 years ago.

Soil Types

Marshes bordering streams such as the Squamscott River and the Crommett and Lubberland Creeks are generally sulfihemists. The fringing marshes, common around the bay, also have sulfihemist soils of varying thicknesses and overlaying a variety of substrata. The sulfihemist soil type has slow internal drainage, a very high water table and contains high amounts of organic matter and sulfitic minerals.


caption Great Bay Reserve SWMP map. (Source: NOAA)

One focus area for the GBNERR research program is anadromous fish in Great Bay. The New Hampshire Fish and Game Department, which administers the Reserve program, is investigating downward trends evident in monitoring data collected during spring spawning events. The Reserve is actively pursing interested partners to develop future projects examining anadromous fish issues in Great Bay and its tributaries.

The Reserve is currently collaborating on two projects with David Berlinsky at the University of New Hampshire involving anadromous fish in Great Bay tributaries. The first is in the final report stage and examined emigration of juvenile American Shad from the Exeter River. Results from this project were presented in a poster at the Restore America’s Estuaries 2nd annual conference in Seattle, Washington this past September. A second project investigating rainbow smelt egg development and hatching success is just beginning. Water quality issues associated with reduced spawning effort in two Great Bay tributaries will be examined with both lab and field investigations.

System-Wide Monitoring Program (SWMP)

The Great Bay NERR monitors water quality at four continuous stations during the ice free months, and weather year round, as part of the System-Wide Monitoring Program (SWMP). This monitoring is done under a cooperative agreement with the University of New Hampshire Jackson Estuarine Laboratory. Five parameters including temperature, salinity, dissolved oxygen, pH, and turbidity are measured every half hour at each of four locations using YSI 6-series multi-parameter datasondes.

The four datasondes are deployed at mid-Great Bay, and the Lamprey, Squamscott and Oyster Rivers. The weather station collects temperature, barometric pressure, relative humidity, photosynthetically active radiation (PAR), and wind speed/direction.

Monthly grab samples are collected at each site and processed for nutrients as well. Samples are processed for dissolved inorganic nutrients, suspended sediments, particulate organic matter, and chlorophyll a.

The monthly nutrient sampling is conducted at low tide at the mid-Great Bay, Squamscott, Lamprey and Oyster River sites. In addition to the monthly data, sampling is conducted every two hours over a full lunar cycle at the Oyster River location.

The Reserve is working with the Coastal Observing Center at the University of New Hampshire who deployed a monitoring buoy at the mid-Great Bay SWMP site. This buoy was deployed in April 2005 and will provide additional parameters such as in-situ nutrient data, fluorescence, and weather information. All information will eventually be posted on the Gulf of Maine Ocean Observing System (GoMOOS) website.

A biological monitoring project was begun in 2002 with SWMP resources. Dr. Jeb Byers’s and students in his lab have collected and processed data examining larval settlement in the Great Bay Estuary. The New Hampshire Estuaries Project recently funded a grant submitted by Dr. Byers and Brian Smith, Reserve Research Coordinator, to continue this project and use the data as a tool for monitoring invasive species.

Further Reading

Disclaimer: This article is taken wholly from, or contains information that was originally published by, the National Oceanic and Atmospheric Administration. Topic editors and authors for the Encyclopedia of Earth may have edited its content or added new information. The use of information from the National Oceanic and Atmospheric Administration should not be construed as support for or endorsement by that organization for any new information added by EoE personnel, or for any editing of the original content.



(2008). Great Bay National Estuarine Research Reserve, New Hampshire. Retrieved from


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