Protecting & Restoring Long Island's Peconic Bays

Habitat Loss and Degradation

Increasing development pressure and human activities have negatively impacted the natural habitats and the diversity of life in the Peconic Estuary.

The Peconic Estuary is home to some of the most valuable and rare habitats in the world. Un­fortunately, ever increasing development pressure and human activities have negatively impacted the natural habitats and the diversity of life in the region. Physical alterations to the environment such as navigational channel dredging, filling of low-lying areas including wetlands, hardening of the shoreline (i.e., bulkheads and other erosion control structures) and clearing of land for roads and buildings all directly impact the habitats and living resources within and around the estuary. These physical alterations, along with pollution and climate change, have led to the loss and degradation of critical habitats including eelgrass beds, wetlands, and diadromous fish habitat within riverine systems.

Threats to Eelgrass>>>

Threats to Wetlands>>>

Threats to Diadromous Fish Habitat>>>

Threats to Eelgrass

Boat propeller harming an eelgrass bed.

Boat propeller harming an eelgrass bed.

Because eelgrass is found in shallow, nearshore waters and requires good water quality and high light penetration,  it is particularly susceptible to human disturbance. Eelgrass beds were drastically reduced in the early 1930s due to wasting disease (caused by the slime mold, Labyrinthula) and further reduced in the 1980s and 1990s due to the harmful algae bloom, Brown Tide, which reduced light penetration to eelgrass. While wasting disease and Brown Tide blooms are not a significant problem in the Peconic Estuary today, other harmful algae blooms are present in the estuary and can reduce light penetration to eelgrass. Additionally, eelgrass habitats are also harmed by boating and fishing activities, alterations to the shoreline, increasing water temperatures, and water pollution.

A 2014 aerial survey identified less than 90 eelgrass beds covering under 1,000 acres, compared to 8,700 acres in 1930 and 1,550 acres and 119 eelgrass beds in 2000. The loss of eelgrass affects all of us who live and recreate on Long Is­land. Without eelgrass, finfish and shellfish populations dramatically reduce. Loss of eelgrass also reduces the estuary’s natural buffering capacity for storm energy.

A map of the changes in extent of seagrass cover between 2000 and 2014 in the Peconic Estuary. 

Threats to Wetlands

Tidal wetlands, areas where the land meets the sea, are among the most productive habitats on earth. Tidal wetlands include vegetated salt marshes and mud or sand flats. Between 1974 and 2005 the Peconic Estuary lost approximately 10 percent of its vegetated tidal wetlands, with the greatest losses occurring in East Hampton and Shelter Island. Eighty-six marsh complexes, out of 159 identified in the Peconic Estuary, are categorized as “at risk.” Tidal wetland loss means reduced feeding, breeding, and nursery habitats for waterfowl, wading birds, shorebirds, fish and invertebrates. It also means a reduction in important ecosystem services, such as sediment retention, nutrient and organic matter recycling and storm and flood buffers.

Percent Change in Marsh Areas within the Peconic Estuary Watershed from 1974 to 2005.

Why are wetlands disappearing?

Land use activities adjacent to wetlands such as developments, dredging and hardening of the shoreline,Dredging equipment in the Peconic Estuary. over time have degraded wetland habitats. Rising seas also threaten to drown marshes. Marshes can migrate inshore gradually with rising water levels, but the rate at which the sea-level is rising is making it difficult for them to migrate inshore fast enough. Additionally, in some cases natural or man-made barriers may prevent marshes for migrating inland. Other threats to marsh habitat include excess nitrogen, the introduction of pollutants, and invasive plants that outcompete with native marsh plants.

Threats to Diadromous Fish Habitat

The Peconic River and other streams, creeks and lakes found within the Peconic Estuary watershed provide critical spawning and maturation habitat for local diadromous fish species. Diadromous fish are those that spend part of their time in freshwaters and part of their time in the ocean.

Grangebel Park Dam in Riverhead prior to Fish-way construction in 2010.

Grangebel Park Dam in Riverhead prior to Fish-way construction in 2010.

In the late 1800s and early 1900s, dams were built on nearly all of Long Island’s freshwater tributaries for grist mills, cranberry bogs, other industrial uses, and as property line demarcations. These dams cut off historic migratory routes for diadromous fish, namely river herring and American eel, blocking access to hundreds of acres of habitat. Other physical structures, such as road culverts, can also block access to freshwater habitats for diadromous fish. River Herring and American Eel populations have been declining over the past century, in part due to this loss of freshwater habitat.


River Herring


River herring is the collective term for two species of fish: Alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis). Mature river herring enter streams and rivers in early spring to spawn and then emigrate back to the marine environment shortly thereafter.

The juveniles grow throughout the
summer in the freshwater environment and then move into the estuary in the fall before heading out to the ocean. River herring provide many vital ecosystem services throughout their life cycle, including filtering the water column and serving as prey for commercially and recreationally important fish such as striped bass and bluefish, and predatory birds like osprey and bald eagles. The American eel has the opposite life cycle to river herring. It spends nearly all of its life in freshwaters, and then migrates out to the middle of the Atlantic Ocean to reproduce and die. PEP is working with partners to provide access for diadromous fish to upstream habitats along the Peconic River.

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