K-12 Teaching and Learning From the UNC School of Education

LEARN NC was a program of the University of North Carolina at Chapel Hill School of Education from 1997 – 2013. It provided lesson plans, professional development, and innovative web resources to support teachers, build community, and improve K-12 education in North Carolina. Learn NC is no longer supported by the School of Education – this is a historical archive of their website.

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Related pages

  • Eastern 4-H Environmental Education Center: Located a few miles outside Columbia, North Carolina, the center provides programming dealing with ecology, ecosystems, and animals and their habitats to area school groups.
  • North Carolina Aquariums: Visit one of the three North Carolina Aquariums and learn about the "diverse natural and cultural resources associated with North Carolina's ocean, estuaries, rivers, streams, and other aquatic environments."
  • Roanoke/Cashie River Center: Open Tuesday-Saturday, this is a great place to take students to learn more about the wetlands and the history of the area.

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Estuaries are places near the coast where freshwater and saltwater mix. Influenced by ocean forces yet partly sheltered from them, estuaries have unique and fascinating ecologies. This article explains what estuaries are, their geology and role in the larger ecosystem, and the ways in which they are currently threatened.

What is an estuary?

The definition of an estuary varies as each estuary is unique in its own way. The simplest definition of an estuary is any place where freshwater joins and mixes with saltwater. But more typically, an estuary is defined as a partially enclosed coastal body of water, having an open connection with the ocean (for example, via a river), where freshwater from inland is mixed with saltwater from the sea. Estuaries typically occupy coastal areas where effects from the ocean are reduced but still influential. Forces like tides, waves, and major storms from the sea play a vital role in an estuary’s development and morphology as they provide energy to help mix the fresh and salt waters and distribute sediments. This mixing creates a brackish (slightly salty) environment where the salinity in the water is between 0.5 and 30 grams of salt per liter, or 0.5 to 30 parts per thousand (ppt or ‰).

Estuaries contain salt water and fresh water in different proportions over the length of the estuary and over the course of the day, with more salt water during high tide and less at low tide. Because they are shallow (in North Carolina, less than thirty feet deep), sunlight penetrates the water, allowing plants to grow. The rivers that feed the estuaries deposit sediments rich in nutrients, which settle onto the sand and mud of the estuary floor. These conditions create unique habitats for both plants and animals, and provide an environment for biological diversity in species (of fish, shrimp, crabs, clams and oysters) that are able to adapt to the brackish conditions. Estuaries are also good nurseries as they provide a place for these species to hatch and grow before they migrate to the sea to live out their adult lives. It was estimated in 1967 that 80–90% of the Atlantic and Gulf coasts had estuaries. This number has drastically declined over the years due to human development and population growth along the coast, and farming, for example.

The barrier islands strung along the coast of North Carolina have created an extensive system of estuaries, with a surface water area of about 3,000 square miles. The only larger estuarine system in the United States is Chesapeake Bay.

Types of estuaries

North Carolina’s estuaries can be divided into trunk estuaries, tributary estuaries, and back barrier sounds.

Trunk estuaries
Trunk estuaries run perpendicular to the coast, in line with the rivers that feed them.
Tributary estuaries
Tributary estuaries flow into trunk estuaries.
Back barrier sounds
Back barrier sounds lie parallel to the coast, between the mainland shore and the barrier islands.

The largest North Carolina estuary is Pamlico Sound. Water drains into this system from eastern North Carolina and southeastern Virginia, from the Chowan, Roanoke, Pasquotank, Pamlico, and Neuse Rivers, from marshes, swamps, forests, and grasslands.

Why estuaries are important

Estuaries help control erosion and reduce flooding of the mainland. Sand bars buffer the impact of waves, while plants and shellfish beds anchor the shore against tides. Swamps and marshes take the initial impact of high winds moving in from the ocean, soak up heavy rain and storm surges, and release the extra water gradually into rivers and groundwater supplies.

Estuaries are a type of environmental filter as plants and animals in estuaries filter pollutants out of the water. Particles in the water are either removed by chemical processes (aerobic respiration, sulfate reduction, methanogenesis) or by the feeding of estuarine animals and bacteria. For instance, salt marsh plants trap some of the chemicals and pathogens carried by rivers and move them into soils where they can be neutralized. Oysters filter impurities out of water as they eat, collecting the contaminants in their bodies. One oyster can filter twenty-five gallons of water per day. Bacteria eat organic matter found in the sediment and in turn release carbon dioxide, hydrogen sulfate and methane into the atmosphere preventing these gases from being excessively stored up in the estuary. However, toxins can accumulate in estuaries causing many environmental and health problems. (This is discussed more below in “Threats to the estuarine system.”

Three quarters of the fish caught commercially in the United States live in estuaries, meaning that on average, estuaries produce more food per acre than our most productive farmland. About thirty commercial fishing species live in North Carolina estuaries. Commercial fishing is important to the national economy and food supply.

And of course, beaches lie along the estuaries of North Carolina — beaches where many of us go every summer to lie in the sun, swim, surf, boat, and fish. Tourists come from across the state and from other parts of the country, and tourism supplies much-needed jobs on the North Carolina coast.

Fish and wildlife

Although estuaries create unusual and changeable habitats, many plants and animals have adapted to the brackish conditions there. More than 150 species of fish and invertebrates live in North Carolina estuaries. Some species use different habitats within the estuarine system during different stages of their life cycles. As in any ecosystem, the plants and animals in an estuary are richly interconnected, and every species depends on several other species to survive.

Oysters and clams attach to gravel and old shells on the shoreline, forming spiky oyster beds that help protect the land from erosion. Blue and stone crabs and grass shrimp hatch in the oyster beds and begin to grow there, eating phytoplankton. The environment these species grow in are also protected from the ocean currents. Black sea bass and flounder forage for food among the oysters.

Swamps and marshes along the edges of the coast provide feeding grounds and shelter for many adult fish and shellfish. Cypress, tupelo, and swamp maple trees grow in swamp forests, whereas grasses such as black needlerush and cordgrasses predominate in salt marshes. Freshwater marshes support cattails, bullrushes, and reeds. River herring spawn in the swamps, while adult river herring, Atlantic menhaden, and bluefish live in the open water.

Underwater plants cover about 200,000 acres on the coast of North Carolina. Submerged plants produce oxygen and nutrients used by animal species. Spotted sea trout, red drum fish, and pink shrimp spend their early lives among the underwater plants, and predators such as flounder and rays hunt there. Bay scallops attach to the blades of plants. Spots, croakers, mullets, and sturgeon feed on algae and tiny animals on the soft floor of the estuary. Flounder, shrimp, and kingfish hatch there, and clams and worms burrow into the mud and sand.

Migratory birds, including tundra swans, sea ducks, and snow geese, winter along the estuary. Egrets and herons fish in the salt marshes. Loggerhead sea turtles hatch on the beach and head out to Pamlico Sound to feed.

A number of birds and animals in danger of extinction depend on North Carolina’s estuaries. Threatened species living in the estuarine system include the green sea turtle, loggerhead sea turtle, bald eagle, and piping plover. Three other species of sea turtle, the roseate tern, and the West Indian manatee are classified as endangered, meaning that they are at more immediate risk of extinction. Red wolves were declared extinct in the wild in 1980, but red wolves bred in captivity were reintroduced in North Carolina beginning in the Alligator River National Wildlife Refuge in 1987. Eight wildlife refuges have been established along the North Carolina coast to protect the habitats of animals and birds.


North Carolina estuarine environments were formed over many tens of thousands of years as sediment from the erosion of the land and mountains were carried to the coastline by rivers and wind, and sediment that was eroded and deposited during rising and falling sea levels accumulated.

The land under the North Carolina estuaries south of Cape Lookout, which include those fed by the White Oak, New, and Cape Fear Rivers, is composed primarily of sediment (rock) laid down between the Upper Cretaceous and Pliocene periods, 90 million to 1.6 million years ago. Harder rocks such as sandstone and limestone predominate. At some point, geologic forces caused these rock units to rise slightly and tilt. They now slope at an average of three feet per mile and are covered by only a thin layer of sand and mud.
A much thicker layer of sediments underlies the larger estuaries north of Cape Lookout. The sand, mud, and peat of the northern estuaries were deposited as ice ages caused the sea level to rise and fall repeatedly over the past 1.6 million years. Because the sea floor slopes less dramatically in the northern part of the state (about 0.2 feet per mile), longer barrier islands have formed.

Threats to the estuarine system

The complex ecosystem of North Carolina estuaries is harmed by changes to the land bordering and surrounding the estuaries and by contamination of river and ocean water. Although the North Carolina estuaries contain 3,000 square miles of surface water, 30,000 square miles of land drains into the Albemarle-Pamlico system. As land is developed for human habitation and use, roads, bridges, culverts, sewage systems, pipelines, and dams change the flow of water through the ecosystem. Whereas wetlands soak up water like a sponge and settle contaminants in the ground, asphalt and concrete deflect water so that it runs off with all its contaminants directly into the rivers, estuaries, and the sea.

Wetlands were drained for logging and farming before the current restrictions on wetland development were enacted. Since European colonization, nearly half North Carolina’s wetlands have been lost, and coastal development continues to damage wetlands. Logging eliminated the old-growth longleaf pines that originally covered the coast of North Carolina. The loblolly pines now seen in patches along the shore are a nonnative species.

Dredging of channels to allow large boats to pass through or dock damages plants and oyster beds and stirs up sediment that clouds the estuary water, and increases sediment deposition in the estuary creating a situation where more dredging has to occur to remove the accumulation. When sediment is suspended throughout the water, fishes’ gills can become clogged, contaminants previously settled in the soil are taken in by fish, and predators have a hard time seeing their prey. Fishing gear that digs into the floor of the estuary or channels cut for irrigation or flood control also increase water turbidity.

Global warming is causing sea levels to rise. Rising sea levels threaten the swamp forests, which can withstand only temporary flooding. Hurricanes also cause high water levels, eroding the shoreline and flooding organisms adapted to freshwater with ocean water. Together, sea level rise and storms cause North Carolina wetlands to erode at a rate of about 800 acres per year.

Although this may seem counterintuitive, estuaries can suffer from an excess of nutrients. Sewage treatment plants, septic systems, polluted air, and fertilizers deposit nutrients such as nitrogen and phosphorus in rivers and ultimately in estuaries. High levels of these nutrients can create large growths of algae called algal blooms. Algal blooms block the passage of sunlight through the water, reducing the growth of other plants. When the algae is alive, it produces oxygen, but once it dies its decomposition consumes oxygen. As oxygen levels drop, fish and invertebrates suffocate.

Some microorganisms whose growth is stimulated by excess nutrients are also directly toxic to humans. In 1987, a “red tide” of toxic, reddish, single-celled organisms called dinoflagellates was carried up from Florida on the tide and bloomed off the North Carolina coast. The dinoflagellates accumulated in shellfish and made people who ate the shellfish sick, and so shellfish harvesting was halted for several months. In 1995, the death of five million fish in the Neuse River was attributed to a different kind of toxic dinoflagellate.

Toxic substances (biological and chemical pollutants) and fecal matter run off into rivers, mix with the sediments, and deposit in the estuaries. These substances can harm humans, animals and plants. Toxins include pesticides, herbicides, weed killer, paint, oil and gasoline from vehicles, and manufacturing byproducts (heavy industrial minerals) such as mercury and dioxin. These toxins can accumulate in the estuarine sediment and cause a multitude of problems. Shellfish are particularly vulnerable to toxins in the early stages of their life cycles. Fish in parts of Albemarle Sound have been found to have high levels of mercury and dioxin, and the North Carolina Division of Water Quality has classified these waters as “impaired.”

Excess toxins can cause an overgrowth of plants in an estuary that can suffocate the environment by taking out too much oxygen, which in turn kills fish and other species through asphyxiation. Asphyxiation can also occur in an estuary when there is an extreme stratification between the freshwater and the saltwater. This can be caused by storms, by excess river runoff, or by slow circulation of the estuarine waters by too much accumulation of sediment. Freshwater is more buoyant than saltwater, so it will “float” to the top and “sit” on top of the heavier salty water. When there is an extreme between the two layers and mixing is not occurring at a fast enough rate, you can get anoxic (very low to no oxygen) conditions in the lower saltier layer near the bottom. This leads to asphyxiation of fish, microorganisms and bottom dwelling species, and promotes the growth of oxygen-consuming bacteria.

Fecal matter from humans and animals also pollutes estuarine waters. Human waste runs into rivers, estuaries and the sea when septic and sewage systems are overloaded. Bacteria, viruses, and parasites that transmit diseases to humans are carried in human waste. In North Carolina, another major pollution concern is fecal matter from hog farms. In 1995, 25 million gallons of hog waste overflowed its barrier on the farm and spilled into the New River, killing huge numbers of fish. According to the 2006 list of bodies of water classified as impaired by the North Carolina Division of Water Quality, shellfish harvesting was prohibited in significant areas of Back, Bogue, Stump, Topsail, Middle, Croatan, Roanoke, and Pamlico Sounds due to fecal coliform contamination. Fecal coliform bacteria are normally found in the digestive tracts of humans and animals, and their presence in an estuary indicates contamination by human or animal waste.

We need estuaries to prevent shoreline erosion, buffer the impact of storms, filter and neutralize contaminants, and produce fish and shellfish to feed ourselves and our livestock. We need governmental agencies and nonprofit groups to monitor and protect water quality and estuarine habitats. A few of the organizations responsible for protecting North Carolina estuaries are listed in the links below.

North Carolina estuaries

Northern back-barrier sounds

  • Core Sound
  • Pamlico Sound (largest)
  • Roanoke Sound
  • Croatan Sound
  • Currituck Sound

Northern trunk estuaries

  • Albemarle Sound estuary
  • Pamlico River estuary
  • Neuse River estuary

Southern back-barrier sounds

  • Back Sound
  • Bogue Sound
  • Stump Sound
  • Topsail Sound
  • Middle Sound
  • Myrtle Sound

Southern trunk estuaries

  • North estuary
  • Newport estuary
  • White Oak River estuary
  • New River estuary
  • Cape Fear River estuary

Tributary estuaries

  • Trent River estuary
  • Bath Creek estuary
  • Scuppernong River estuary
  • South River estuary
  • Bay River estuary
  • Pungo River estuary
  • Alligator River estuary
  • Pasquotank River estuary
  • North River estuary


  • American Oceans Campaign (1996). Estuaries on the Edge: The Vital Link Between Land and Sea. Washington, DC: American Oceans Campaign.
  • North Carolina Division of Marine Fisheries. “Fish habitat information.” Accessed July 10, 2006.
  • U.S. Fish and Wildlife Service. County Species List for North Carolina, March 2006.
  • O. H. Pilkey et al (1998). The North Carolina Shore and Its Barrier Islands: Restless Ribbons of Sand. Durham, NC: Duke University Press.
  • Developments in Sedimentology 53: Geomorphology and Sedimentology of Estuaries, Ed. G.M.E. Perillo, Elsevier Science Publishers B.V., Amsterdam, The Netherlands: 1995.
  • D. Frankenberg (1997). The Nature of North Carolina’s Southern Coast: Barrier Islands, Coastal Waters, and Wetlands: An ecotourist’s guide to the North Carolina coast, from Portsmouth Island to Calabash. Chapel Hill, NC: University of North Carolina Press.