Where We Work

Our Region

Our Watershed and its Estuaries are truly special places

Piscataqua Region Watershed

A watershed is an area of land where all the water from rain and snow drains into a common body of water, like a river, bay, or ocean. Our waterways are deeply connected, even if they are miles apart. From Wakefield, New Hampshire to Kittery, Maine, our watershed is like a big bowl that catches all the water and channels it to one place: the ocean.

The Piscataqua Region Watershed spans 52 cities and towns (42 in New Hampshire and 10 in Maine) that drain to the Piscataqua River, Hampton-Seabrook Estuary, or the Atlantic Ocean. The water in our 1,086 square mile watershed connects us all, from headwaters* to our estuaries in Great Bay and Hampton-Seabrook.

Click on the map to the right to see a larger picture of our watershed.

*Headwaters are the starting points of rivers or streams, often found in small creeks, ponds, or lakes high up in a watershed.

Our Estuaries

An estuary is a place where fresh and saltwater meet and mix together. These diverse ecosystems are places we fish, swim, kayak, birdwatch, or simply walk along a marshy shoreline. Estuaries are homes to nature and people alike. As natural nurseries, they provide homes for diverse marine life like lobsters, fish, oysters and seagrass, as well as passage for migratory fish. For people, they offer recreational opportunities and inspire a deep connection to nature. Estuaries also play a vital role in protecting communities from storms and floods, making them a critical part of both ecological and human life. In our watershed, Great Bay and Hampton-Seabrook are two nationally significant estuaries.

The Great Bay Estuary drainage area is 1,023 square miles, with 242 miles located in Maine. The total tidal shoreline is 204 miles from the mouth of Portsmouth Harbor to the head of tide of all tributaries at high tide. The tidal estuary has a surface area of 21 square miles. There are eight main tributaries to the Great Bay including the Winnicut, Squamscott, Lamprey, Oyster, Bellamy, Cocheco, Salmon Falls, and Piscataqua rivers that flow through 38 communities in New Hampshire and 10 in Maine.

Seven major rivers flow into the Great Bay Estuary:

Winnicut
Exeter/Squamscott River
Lamprey River
Oyster River
Bellamy River
Cocheco River
Salmon Falls River
Great Works River

Other important information:

The Great Bay Estuary covers 1,023 square miles; 776 square miles are in NH and 247 square miles are in ME.
60% of the Great Bay watershed is covered by forest.
The Great Bay Estuary is one of the nation’s most recessed estuaries – saltwater from the Gulf of Maine travels 15 miles inland through the Piscataqua River and Little Bay before flowing into Great Bay.
It can take up to 36 tidal cycles, or 18 days, to flush water through the estuary.
169 birds, fish, and plant species use the Great Bay Estuary in different ways at different times. 23 of these species are threatened or endangered at the state or federal level.

Find out more about how PREP and our partners are protecting the Great Bay Estuary.

The Hampton-Seabrook Estuary drainage area is 46 square miles with 8 square miles located in Massachusetts (upstream reaches of the Blackwater River). The tidal shoreline of the estuary is 131 miles at high tide and the surface area at high tide is 2 square miles, excluding the salt marsh covered by water during a spring tide. There are seven main tributaries to the Hampton-Seabrook Estuary including the Tide Mill Creek, the Taylor, Hampton Falls, Brown's, Cain's, Little, and Blackwater rivers that flow through seven New Hampshire communities.

Six major rivers flow into the Hampton-Seabrook Estuary:

Taylor River
Hampton Falls River
Browns River
Cains Brook/Mill Creek
Hunts Island Creek
Blackwater River

Other important information:

The Hampton-Seabrook Estuary is a bar-built estuary situated behind barrier beaches and surrounded by 5,000+ acres of salt marsh.
The estuary has an area of approximately 475 acres at high tide.
Approximately 72 miles of shoreline make up the Hampton-Seabrook Estuary.
The Hampton-Seabrook Estuary has the last remaining sand dunes in coastal New Hampshire.
Hampton-Seabrook Harbor has the most productive clam flats in New Hampshire.

Find out more about PREP + our partners are protecting the Hampton-Seabrook Estuary

Critical Species

The critical species that have been identified as important to our estuaries include soft-shell clams, American oysters, Eastern brook trout, migratory fish, shorebirds, salt marsh breeding birds, and eelgrass. Robust populations of these species are good indicators of estuarine, marsh, and watershed health. Learn about each of these species below.

Primarily found in the Hampton-Seabrook Estuary, although they exist in the Great Bay Estuary as well.
An important economic, recreational, cultural, and natural resource for the Seacoast region.
Recreational shellfishing in the Hampton-Seabrook Estuary is estimated to contribute more than $3 million a year to the New Hampshire economy.
Predators (primarily green crabs), disease, and recreational harvest pressures have caused the clam populations to decline.
Periodically, harvesting is limited by the presence of red tide toxins and high bacteria counts.

For the latest information about clams and shellfish harvest opportunities, check out the Clams Indicator in the State of Our Estuaries report.

American Oysters are a keystone species in the Great Bay Estuary due to their many benefits.
As filter feeders, they take in the water around them, filter out some of the pollutants and sediments, and then release cleaner water.
When healthy, an oyster can filter up to 20 gallons of water a day. They play a key role in nutrient cycling by taking up nitrogen in their shells and tissue.
Harvesting and aquaculture farming of oysters provide economic benefits to local communities and businesses.
Oyster shell reefs create important habitats for other creatures in the estuary.
Oyster populations have declined significantly from 1993 to today, because of disease, overharvest, and poor water clarity and quality.

For the latest information about oysters, check out the Oysters Indicator in the State of Our Estuaries report.

Eastern brook trout is the New Hampshire state fish and requires high-quality, cold water streams for spawning and juvenile growth.
They are the only trout native to streams and rivers of the eastern United States and are an excellent indicator of the health of the watersheds they live in.
Development impacts in our headwaters and first-order streams increase water temperatures and degrade water quality, resulting in conditions that do not support native Eastern brook trout.
Improving stream connectivity, protecting low-order streams and their buffers, limiting impervious surfaces (pavement, roofs & roads), and removing pollutants from stormwater runoff will improve the habitat and ensure the future survival of this critical species.

Major rivers of the Piscataqua Region historically had very large populations of migratory fish including Atlantic salmon, river herring, American shad, and American eels.
Today, only river herring and American eels still return regularly in substantial numbers to the rivers and are the focus of current migratory fish restoration efforts. River herring are migratory fish, which means they travel from the ocean upstream to the freshwater streams, marshes, and ponds to reproduce.
Herring are eaten by other species and therefore sustain important commercial and recreational fisheries and other wildlife.
Herring returns are in decline due to water quality decline and habitat degradation, barriers to stream and river connectivity caused by dams and road crossings, as well as overharvesting.
The construction of dams and road-crossing culverts has fragmented and blocked the majority of the freshwater stream habitat historically used by diadromous fish.

To learn more about migratory fish in the region, check out the Migratory Fish Indicator in the State of Our Estuaries report.

The Hampton-Seabrook Estuary– and to a lesser extent Great Bay and the smaller coastal marshes– are critical stopover sites for migratory shorebirds in spring and fall.
During these periods, birds roost and feed on tidal flats, eelgrass leaves and seeds, and marshes.
These birds get critical nutrients and rest for their long journeys to their wintering grounds.
The salt marsh sparrow is a species of special concern in Maine and New Hampshire.
Salt marsh sparrows require a tidal wetland habitat that is dominated by the high salt marsh grass called Spartina patens for nesting and foraging.
A NH Audubon study in 2007 counted more than 800 Salt Marsh sparrow nests in the Hampton-Seabrook Estuary.
Ninety percent of the bird’s breeding range is in the Northeast. Preserving the existing habitat and restoring degraded salt marsh will benefit the salt marsh sparrow.

Eelgrass (Zostera marina) is a rooted vascular plant that can form dense sub-tidal meadows in estuarine waters.
Eelgrass filters nutrients and suspended particles from water and stabilizes sediments.
Eelgrass beds are in decline in the Great Bay Estuary.

To learn more about the condition of eelgrass beds in the Great Bay Estuary, check out the Eelgrass Indicator in the State of Our Estuaries report.

Critical Habitats

Habitats that are critical to the health of our estuaries include freshwater wetlands, streams, eelgrass beds, oyster reefs, and salt marshes. These habitats are threatened by increasing population, declining water quality, invasive species encroachment by development, and climate change. Learn about each of these species below.

Freshwater wetlands store large quantities of water and provide habitat and food for many wildlife species.
They provide a storage basin for rain, snow, and runoff and can be effective at removing pollutants and maintaining clean water.
Water from wetlands is slowly released into streams and rivers and helps sustain these systems in periods of low flow and acts as sponges in periods of flood protecting people and property.
While land protection or local regulations protect some wetland systems from encroaching development, filling, and associated degradation, most wetlands remain vulnerable.
Polluted stormwater runoff from developed areas adjacent to wetlands can negatively impact the hydrology, plant community, and habitat value of freshwater wetlands.

Salt marshes perform many of the same functions as freshwater marshes and are a fundamental part of the estuarine food web.
Salt marshes are critical carbon sinks and capable of adjusting to gradual changes in sea level.
Salt marshes are some of the most productive ecosystems on the planet.
Coastal salt marshes have been proven to be critical in protecting communities from coastal storms and surges.
Since the early 1900s, hundreds of acres of salt marsh have been lost in the Great Bay Estuary and the Hampton-Seabrook Estuary.
Some of this loss is due to direct development and is unlikely to be returned to the salt marsh.

To learn more about the status of salt marshes in our region check out the Salt Marsh Indicator in the State of Our Estuaries report.

Eelgrass (Zostera marina) is found in the Great Bay Estuary and Piscataqua River.
They provide valuable habitat for estuarine species, especially juvenile commercial fish and shellfish species like stripers and lobsters.
Eelgrass beds are a critical component of the estuarine food web and reflect the overall health of estuarine water quality.

To learn more about the health of eelgrass beds in our region, check out the Eelgrass Indicator in the State of Our Estuaries report.

Rivers and streams of an estuary are like veins flowing throughout the system carrying essential nutrients, fish, wildlife, and water.
Smaller streams with intact, undeveloped floodplains and buffers maintain cool water temperatures, provide wood and leaf debris for invertebrate species, and channel formation, retain, and transform nutrients to protect water quality.
They provide connectivity of habitat and recharge and discharge zones for groundwater.
Together with wetlands, they provide food storage, protection of life and property, as well as erosion and sedimentation control.
Rivers and streams in the Piscataqua Region watershed are crossed by multiple roads and are restricted by large and small dams.
Where roads cross waterways, their accompanying infrastructure, culverts, and bridges can inhibit passage by fish, reptiles, amphibians, and mammals, as well as restrict streamflow, resulting in ponding (water backup behind restrictions) or perching (outflow entering above stream level).
These physical restrictions may lead to water quality degradation, road flooding, and failing public infrastructure.

In addition to filtering pollutants and sediment from the water column, oyster shell reefs (or oyster beds) create important habitats for other creatures in the estuary.
These reefs also attenuate wave energy during storm events, ultimately protecting people and property along the shore.

To learn more about efforts to increase the number of oyster beds in the Great Bay Estuary, check out the Oyster Restoration Indicator in the State of Our Estuaries report.

Critical Issues

Our estuaries – and their surrounding landscapes – are impacted directly and indirectly by several stressors. Some of these are slow-acting and chronic while others are episodic. These influences, however, act as stressors and cannot be considered independently of one another. Learn about each of these species below or check out the "Big Picture" section of the State of Our Estuaries report.

Our region is experiencing changing precipitation and more extreme storm events.
Between 2004 and 2009, total annual precipitation levels remained above the 75th percentile.
Since 2012, levels have been below the 25th percentile.
Between 1996 and 2014, extreme precipitation (two inches or more in one day) in the Northeast was 53% higher than it was in the previous 94 years.
The 2006 Mother’s Day Storm alone greatly increased levels of dissolved organic matter and brought salinity levels close to zero for five days.

Coastal acidification has increased as a result of higher levels of carbon dioxide in the atmosphere.
It is magnified by the increased frequency of extreme storms, which bring nutrient-rich freshwater into the coastal system.
Nutrients can promote intense respiration (the digestion of dead algae by microbes), which consumes oxygen and produces carbon dioxide which leads to increased acidification.
This negatively impacts many important species, from blue mussels and oysters to lobsters and flounder. It also has profound impacts on ecosystem health.

Between 1990 and 2010, impervious surfaces in our watershed increased by 120% and have continued to increase over the last five years.
Combined with changes in precipitation, these impervious surfaces are sending more contaminants into our estuaries.
During extreme storm events, they are delivered in large, disruptive pulses. Such rapid inflows of runoff not only add more nitrogen and toxics to the system, they also stir up estuarine sediments.

Nutrients fuel the growth of phytoplankton and seaweed and make it more difficult for light to reach eelgrass beds.
In our system, monthly sampling of phytoplankton levels are most often in ranges considered “good” or “fair,” though sometimes “poor”
Excessive seaweed and phytoplankton growth also can lead to low dissolved oxygen levels.
Low dissolved oxygen events continue to occur in our tributaries, but these are not necessarily caused by excess nitrogen.
Excess nitrogen can lead to the organic enrichment of sediments, which limits the abundance of benthic animals and shellfish and the growth of eelgrass.

Where We Work

Our Region

Piscataqua Region Watershed

Our Estuaries

Great Bay Estuary

Hampton-Seabrook Estuary

Critical Species

Critical Habitats

Critical Issues

2025-2026 PREPA Grants: Request for Proposals

2024-2025 PREPA Grants: Celebrating Five Local Community Projects Making an Impact

Unlocking Grant Opportunities: Simplifying the Path for Community Resources

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