Critical Habitats

Habitats that are particularly critical to the health of the Piscataqua Region estuaries include freshwater wetlands, streams, eelgrass beds, oyster reefs and saltmarsh. These habitats are threatened by rapid human population expansion, declining water quality, invasive species, encroachment by development and climate change. Let’s explore these critical habitats a bit more.

Freshwater wetlands

Freshwater Marsh, Raymond, NH

Freshwater Marsh, Raymond, NH

Freshwater wetlands store large quantities of water and provide habitat and food for a multitude of 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 to streams and rivers and helps sustain these systems in periods of low flow and act 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


New Hampshire’s largest salt marsh system in Hampton-Seabrook, NH

Salt marshes perform many of the same functions as freshwater marshes and are a fundamental part of the estuarine food web. Salt marshes have been shown to be 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 1900’s, hundreds of acres of salt marsh has been lost in the Great Bay estuary and in the Hampton-Seabrook Estuary. Some of this loss is due to direct development and is unlikely to be returned to salt marsh.

Eelgrass (Zostera marina) 


Eelgrass meadow under water.

Eelgrass (Zostera marina) is a rooted vascular plant that can form dense sub-tidal meadows in estuary waters. Eelgrass beds provide valuable habitat for estuarine species, especially juvenile commercial fish and shellfish species like stripers and lobsters are a critical component of the estuarine food web, and reflect the overall health of estuarine water quality. Eelgrass filters nutrients and suspended particles from water and stabilizes sediments. Eelgrass beds are in decline in Great Bay Estuary.

Rivers and Streams

The Islinglass River runs from Strafford through Barrington and Rochester to meet the Cocheco River in Dover, NH

The Islinglass River runs from Strafford through Barrington and Rochester to meet the Cocheco River in Dover, NH

It’s the fresh water from the rivers that meets the salt water of the sea that forms an estuary and so the rivers and streams of an estuary are like its 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 and habitat and recharge and discharges zones for groundwater. Together with wetlands they provide flood storage and protection of life and property and 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 enters above stream level). These physical restrictions may lead to water quality degradation, road flooding and failing public infrastructure. There are 17 head of tide dams blocking most major and minor tributaries to the estuaries and the ocean. These dams have eliminated a natural transition zone between saltwater and freshwater and have thereby almost completely eliminated important brackish marsh habitats as well restricted passage for diadromous fish (migratory fish who spend some part of their life cycle in salt and fresh water).

American oysters

Oyster spat on shell is how oysters start to form reefs in Great Bay, NH

Oyster spat on shell is how oysters start to form reefs in Great Bay, NH

Oysters are a keystone species in the Great Bay Estuary because they provide 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 taking up nitrogen into their shells and tissue. Harvesting and aquaculture farming of oysters provide economic benefits to local communities and businesses. Oyster shell reefs also create important habitat for other creatures in the estuary. Oyster populations have declined significantly from 1993 to today. There was 1,100 acres of oysters in the bay in 1993 and now there is only 100 acres. Disease, overharvest and poor water clarity and quality are likely to blame.

UNH CE Habitat Brouchures

Click here to download
the UNH Cooperative Extension

Habitat Stewardship Brochures
for all of these Critical Habitats

PREP is part of the U.S. Environmental Protection Agency’s National Estuary Program, a joint program between local, state and federal agencies established under the Clean Water Act with the goal of protecting and enhancing nationally significant estuarine resources. PREP is supported in part by an EPA matching grant and is housed within the School of Marine Science and Ocean Engineering at the University of New Hampshire.