Protecting & Restoring Long Island's Peconic Bays

Habitats & Wildlife

PEP will build scientific understanding and support decision-making to address threats to habitat and species.

Healthy Ecosystem with Abundant, Diverse Wildlife

The Peconic Estuary is home to some of the most valuable and rare habitats in the world. Physical alterations to the Peconic Estuary and its watershed such as navigational channel dredging, hardening of the shoreline with bulkheads and other erosion control structures, and clearing of land for roads and buildings all harm the habitats and living resources within and around the Estuary. At the headwaters of the Peconic River, the sensitive pine barrens ecosystem protects important drainage areas to the aquifer, which eventually outfall into the main estuary system. These alterations, along with pollution and climate change, have led to the loss and degradation of critical habitats such as the pine barrens, eelgrass beds, marshes, and diadromous fish habitat.

The habitats of the Peconic Estuary face several key threats:

  • Development and other human activities have resulted in habitat loss, fragmentation, and degradation, and remaining open space is under increasing development pressure.
  • Dams built on streams flowing into the Peconic Estuary prevent the movement of diadromous fish into freshwater.
  • Invasive species often outcompete native plants and animals, threatening biodiversity and reducing habitat value.
  • The interacting effects of rising seas and lack of sediment threaten to drown tidal wetlands and shoreline habitats, especially if they cannot migrate inland due to natural or manmade barriers.
  • Nitrogen pollution, warmer water temperatures, and human disturbance are contributing to the loss of eelgrass beds within the Peconic Estuary.

Threats to Critical Peconic Habitats

Eelgrass Beds
Once bountiful throughout the Peconic Estuary, eelgrass has declined significantly over the last century. In 1930, there were more than 8,700 acres of eelgrass beds in the estuary. In 2014, less than 1,000 acres remained—a decline of more than 85 percent. Aside from a meadow in Bullhead Bay, no eelgrass persists in the Peconic Estuary west of Shelter Island. Loss of eelgrass beds affects the many commercial and recreational fish and invertebrate species that rely on them for food and shelter. An eelgrass disease epidemic along the Atlantic seaboard in the 1930s and a series of harmful algal blooms in the Peconic Estuary in the 1980s and 1990s were major factors in the loss of eelgrass habitat. Globally, seagrasses have decreased dramatically in the last few decades, and climate change is believed to play a major role. Warmer water temperatures stress eelgrass and may render historical locations of eelgrass beds no longer suitable for eelgrass growth. Boat propeller harming an eelgrass bed. Long-term monitoring in the Peconic Estuary indicates that water temperatures in the western section of the estuary no longer fall within the optimal range for eelgrass. Rising sea level is another important climate-related threat to eelgrass survival in locations where seawalls and other types of shoreline hardening make it impossible for eelgrass beds to shift landward to remain in a favorable water depth. In addition, nutrient enrichment, algal blooms, water quality, boating and fishing practices, and shoreline stabilization structures are all collectively threatening the health and extent of eelgrass. The picture shows a boat propeller harming an eelgrass bed. Over the last decade eelgrass restoration has been attempted at multiple sites within the Peconic Estuary with limited success. A further understanding of suitable environmental conditions for eelgrass growth is needed to better inform eelgrass protection and restoration efforts.
Tidal Wetlands
Tidal wetlands are among the most productive and ecologically valuable habitats on Earth. Between 1974 and 2005, the Peconic Estuary lost approximately ten 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, have been categorized as at risk (defined as marsh loss greater than ten percent). The below image shows the Percent Change in Marsh Areas within the Peconic Estuary Watershed from 1974 to 2005. Of particular concern is the rapid decline of approximately 25 percent of high marsh habitat between 1974 and 2005. These trends suggest significant marsh drowning is occurring. Marsh drowning is related to the interacting effect of the failure of marsh accretion processes (such as deposition of organic sediments and accumulation of plant biomass) to keep pace with sea-level rise. Hardening of the shoreline, excess nutrients, tidal restrictions, and other land and human-use activities all affect marsh accretion and erosion processes and contribute to the degradation of these habitats. Marshes can migrate inshore gradually with rising sea levels, but the rapid rate at which sea level is now rising makes it difficult for them to migrate inshore fast enough. Additionally, in some cases, natural or man-made barriers—such as seawalls and other hardened shoreline structures—will prevent marshes for migrating inland. Another significant reason for the loss of native high marsh communities in the Peconic is the invasion of the common reed, Phragmites australis. An 88.5 percent increase in Phragmites australis was recorded in the Peconic between 1974 and 2005. 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 buffering. Other threats to marsh habitat include excess nitrogen, the introduction of pollutants, and other invasive plants that outcompete with native marsh plants.
Diadromous Fish Habitat
The Peconic River and the other streams, creeks, and lakes in the Peconic Estuary’s watershed provide critical spawning and maturation habitat for diadromous fish species. Diadromous fish are those that spend part of their life cycle in freshwater and part in the ocean. River herring is the collective term for two species of fish: Alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis). Below is a picture of an Alewife. River Herring In the late 1800s and early 1900s, dams were built on nearly all of Long Island’s freshwater tributaries for grist mills, cranberry bogs, and other industrial uses, and as property line demarcations. These dams cut off historic migratory routes for diadromous fish, notably river herring and American eels, blocking access to hundreds of acres of habitat. Other physical structures such as road culverts can also block access to freshwater habitats. River herring and American eel populations have declined over the past century, in part due to this loss of freshwater habitat. The decline of these diadromous fish has negative impacts on the health of the Peconic Estuary ecosystem. The movement of diadromous fish from salt to fresh water is especially important in transferring ocean-derived energy into estuarine, freshwater, and upland habitats. River herring and American eel also provide prey for countless species during their annual migration. The Peconic Estuary Partnership has been working with its partners to restore historic access to freshwater habitat for diadromous fish by installing fish passage structures that allow fish to go around or over the dam, and replacing undersized road culverts with larger, fish-friendly culverts. See this page for more information on the PEP's efforts to expand diadromous fish habitat in the watershed.

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

Current Projects

Peconic Estuary Partnership provides program and project updates!

Search here for PEP Program Updates

PEP Habitat Restoration Plan & Map

In 1997 the Peconic Estuary Partnership Habitat Restoration Workgroup was formed and charged with identifying important Peconic natural habitats with enhancement or restoration potential, developing overall habitat restoration goals, and identifying and prioritizing potential restoration projects. The end product was the “Habitat Restoration Plan for the Peconic Estuary” dated December 2000. This Habitat Restoration Plan was subsequently updated in 2009, in 2017 and again in 2020. Over the years, the Peconic Estuary Partnership has completed projects to restore a variety of habitat types, including beaches/dunes, grasslands, diadromous fish habitat, eelgrass, and wetlands.

Peconic Estuary Partnership 2020 Habitat Restoration Plan

View Habitat Restoration Project Map

Woodhull Dam Fish Passage Construction

The Woodhull Dam is the next major barrier to fish passage on the Little River. Providing permanent fish passage at Woodhull Dam will create access to 95 acres of prime spawning habitat within Wildwood Lake. Wildwood Lake is located within preserved lands and would provide high quality, protected habitat. Funding for the construction of the dam was awarded to Suffolk County Parks/PEP through a NYSDEC Water Quality Improvement Project (WQIP) Grant, the Suffolk County Water Quality Protection and Restoration Program (WQPRP) grant and the United States Fish and Wildlife Service (USFWS). The project includes the construction and installation of a combination Denil pass and step pool fish passage and eel passage through the dam bypassing the existing culvert, with a video monitoring and fish counter system.

Click here to Learn about PEP’s Progress in Diadromous Fish Habitat Restoration. See below for the fish and eel passage design:

Upper Mills Dam Fish Passage Design

The Upper Mills Dam is the next major barrier to fish passage on the main stem of the Peconic River. In addition to the dam, USGS maintains a concrete weir two-hundred and fifty (250) feet downstream of the dam in order to measure the stage and discharge of the Peconic River, which also impedes fish passage. A feasibility and alternative analysis for fish passage at the Upper Mills Dam was completed in 2011. PEP is currently contracting with L.K. Mclean Associates P.C. to complete the engineering design and permitting services for construction of a fish passage at the Upper Mills Dam and Weir. This project will open 40 acres of historic spawning and maturation habitat for diadromous fish. The fish passage engineering design and permitting work is expected to be complete in August 2021.

Click here to Learn about PEP’s Progress in Diadromous Fish Habitat Restoration. PEP is currently developing engineering designs for selected design alternative below:

SCMELC Demonstration Living Shoreline Project

Peconic Estuary Partnership is working with Cornell Cooperative Extension of Suffolk County to complete a demonstration living shoreline project at the Suffolk County Marine Environmental Learning Center (SCMELC) in Southold, NY. The project incorporates smooth cordgrass and ribbed mussels and will be evaluated to determine its ability to provide storm resilience and coastal habitat, but also the shoreline’s effectiveness in reducing nitrogen and pathogen inputs to the Peconic Estuary. The project is expected to be complete in August 2021. See here for the SCMELC Living Shoreline project page.

Meetinghouse Creek Wetland Restoration Project

In 2019 PEP completed a conceptual design, with Land Use Ecological Services, Inc.,  for the priority habitat restoration project at Meetinghouse Creek, Riverhead, NY. Click here for the Meetinghouse Creek Wetland Restoration/ Construction Conceptual Design Plan.

This site is located at a large wetland area that forms the headwaters to Meetinghouse Creek in Riverhead, NY. Meetinghouse Creek is listed as an impaired waterbody on the NYSDEC Priority Waterbodies List. The wetland vegetation at this site is dominated by Phragmites.

The conceptual design recommendation is to construct a 1.2-acre stormwater wetland to treat stormwater runoff in the 5.6 acre contributing watershed. This will improve water quality in the downstream wetland and surface waters. Additionally, it will greatly increase the ecological quality of the habitat and improve plant and wildlife diversity.

PEP is working through NEIWPCC to complete Engineering Design and Permitting for the habitat restoration project. PEP will work with our contractors, Interfluve and Land Use Ecological Services, Inc., and Town of Riverhead to complete the Engineering Design and Permitting services, which are anticipated to be complete December 2022.

Narrow River Road Wetland Restoration Project

In 2019 PEP completed a conceptual design, with Land Use Ecological Services, Inc.,  for the priority habitat restoration project at Narrow River Road, Southold, NY. Click here for the Narrow River Road Wetland Restoration Conceptual Design Plan.

Narrow River is a tributary of the Peconic Bay and flows south from the Town’s Whitcom Marsh Preserve under Route 25 and along the eastern side of Narrow River Rd in Orient, NY. An earthen dam was constructed after the 1938 hurricane to prevent tidal flooding of the lands north of the dam. The westernmost section of the dam blocked the tidal flow from Narrow River to the large meadow area north of the dam known as Broad Meadows and Whitcom Marsh Preserve north of Route 25.

Remediation of the culvert and earthen dam is needed to improve the tidal exchange throughout the extent of the river and increase the salinity of the river to promote the re-establishment of native vegetation and important waterfowl and wading bird habitat. The potential extent of the restoration area is 80 acres. PEP is working with partners to secure funding for engineering design plans and construction.

Lake Montauk Alewife Access and Habitat Enhancement Project

In 2019 PEP completed a conceptual design, with Land Use Ecological Services, Inc.,  for the priority habitat restoration project at Lake Montauk, East Hampton NY. Click here for the East Hampton: Lake Montauk Alewife Access and Habitat Enhancement Conceptual Design Plan.

The goal of the  conceptual habitat restoration design plan is to restore connectivity for diadromous fish species between Lake Montauk and Big Reed Pond by replacing an undersized culvert, and between Lake Montauk and Stepping Stones Pond by replacing an undersized, impassable culverts under Old West Lake Drive and removing debris.

Suffolk County Capital funds have been secured to replace the culvert that leads to Big Reed Pond and PEP staff will be working with Suffolk County parks to complete the permitting and construction. PEP staff are also working with partners to secure funding to complete engineering design plan and construction of the culvert leading to Stepping Stones Pond.

Widows Hole Living Shoreline Project

PEP worked with Peconic Land Trust and Cornell Cooperative Extension (CCE) of Suffolk County to create a living shoreline on Peconic Land Trust's Widow's Hole Preserve in Greenport, NY. This is the first living shoreline project to be completed in the Peconic Estuary. It will be monitored to assess its efficacy in providing storm resilience and coastal habitat, and the changes in elevation of the shoreline over time to identify loss/gain of sand and the growth of smooth cordgrass (Spartina alterniflora) and America beachgrass (Ammophila) Click here to view the project story:  Widow’s Hole Preserve Story Map.

Phase II of the project scope, extending the living shoreline to the entire Widows Hole Preserve property, has been developed by CCE and added to the PEP Habitat Restoration Plan.

Paul Stoutenburgh Preserve Habitat Restoration

Paul Stoutenburgh Preserve is a Town owned 52 acre nature preserve on the west side of Arshamomaque Pond with an adjacent 7 acre County owned preserve, Arshamomaque Preserve. Several areas along the shoreline and interior have pockets of invasive Phragmites australis resulting in low quality wetlands. Invasive mile-a-minute weed has become established and is rapidly increasing in areas adjacent to tidal and fresh water wetland areas. The project site was nominated by the Town of Southold to be included in the Peconic Estuary Program Habitat Restoration Plan in 2013 and the project was prioritized for habitat restoration in 2016. Habitat restoration is recommended and is anticipated to involve the removal of the invasive species using currently accepted removal and restoration practices, and changes to drainage infrastructure in the area to make conditions less suitable for invasive vegetation.

The goal of the project is to improve the freshwater and tidal wetland habitat and to promote the re-establishment of native vegetation and important waterfowl, shorebird, wading bird and migratory bird habitat. An RFP for Engineering Design and Permitting will be advertised when Suffolk County Capital Budget funding is made available, or if external grant funding is awarded.

PEP Eelgrass Monitoring and Management Plan

The decline of eelgrass (Zostera marina L.) in the Peconic Estuary over the last 70 years has contrib­uted to the degradation of the estuary as a whole. The PEP has undertaken several initiatives to advance the protection and management of eelgrass in the Peconic Estuary. Since its inception, the PEP has supported a Long Term Eelgrass Monitoring Program conducted by Cornell Cooperative Exten­sion’s Marine Program. This monitoring program, has focused on collecting data pertaining to the health of the eelgrass beds at various sites throughout the Peconic Estuary. PEP also conducted aerial surveys of eelgrass in 2014 to map and identify changes in the extent of the resource over time. In 2009, an Eelgrass Management Plan was adopted to provide a nesting ground for discussion, theories, and new actions necessary to minimize impacts to eelgrass and to provide a suitable environment for eelgrass to exist.

Search here for PEP Long-Term Eelgrass Monitoring Reports and other eelgrass reports

Below are the most recent Long-Term Eelgrass Monitoring Reports:

Peconic Estuary Program 2019 Long-Term Eelgrass Monitoring Program Report

Peconic Estuary Program 2018 Long Term-Term Eelgrass Monitoring Program Report


Seagrass Bio-optical Model

The Seagrass Bio-optical Model has been developed in cooperation with The Research Foundation of SUNY Stony Brook to provide site specific information on what areas of the Peconic Estuary provide suitable habitat for eelgrass to guide future eelgrass protection and restoration projects. This project will lead to a better understanding of specific light and temperature requirements for eelgrass in the Peconic Estuary (PE). This is the critical next step towards understanding the threats to the eelgrass community and where restoration projects have the best probability of success. The final report is linked below:

Living on the edge- Analysis of Zostera marina and the potential for restoration in Peconic Bay (Long Island, NY) (2020)

The Seagrass Restoration Map and Tool will be posted here when available to share the results with our stakeholders.

Click here for the presentation on the final Seagrass Bio-Optical Model: Living on the edge- analysis of Z. marina and potential for restoration- Kaitlyn O'Toole (2020).

Peconic Estuary Ecosystem Study

The PEP is working with the NYSDEC and SUNY Stony Brook to analyze spatial and temporal trends in the Peconic Estuary finfish trawl survey dataset, and develop risk metrics from ecological relationships for the Peconic Estuary that examine whether local and regional environmental changes have increased the vulnerability of individual finfish and mobile invertebrate species, community assemblages, and ecosystem processes.

The ECOSIM is a quantitative modeling framework that can represent all major ecosystem functional groups and can be used to identify and assess structural changes in the ecosystem in response to environmental change. The proposed study will identify vulnerable species, critical habitats, and ecosystem properties within the Peconic Estuary. This information has direct application to decisions affecting the use, management, and conservation of the natural resources in the bay.

A SUNY Stony Brook is advertising for a post-doctoral position currently to complete the work. The expected completion period is March 2023.

Critical Lands Protection Strategy Update

The status and trends of living resources are closely related to the amount of land preserved in the Peconic Estuary. Benefits to land protection include preserving unique species and natural communities, and controlling nutrient and pollution loads to the Estuary. In addition, the public has exhibited a strong attachment to the natural resources and amenities provided by the Peconic Estuary region. The Peconic Estuary Partnership developed a 2004 Critical Lands Protection Strategy (CLPS) that outlined land still available for development that also meet certain criteria used to determine land protection priorities. The Partnership shares this information with State and local agencies so that it can be used to make land acquisition decisions. Since 2006, approximately 2,443 acres of land have been protected in the Peconic Estuary watershed. The most significant source of funding for land protection is the Community Preservation Fund (CPF), administered by the five East End towns. This funding is supplemented by County and State governments, and not-for-profit organizations (especially The Nature Conservancy and the Peconic Land Trust). In 2019 the Critical Lands Protection Strategy was updated to continue protecting land for habitat and water quality protection, adaptation to sea level rise and groundwater protection. PEP worked with Anchor QEA, LLC. to re-evaluate the original prioritization of the Critical Lands Protection Strategy (CLPS) and the lands within the watershed were evaluation and prioritized considering climate change impacts. The 2019 Critical Lands Protection Strategy is included here in the 2019 Peconic Estuary Partnership Climate Vulnerability Assessment and Action Plan.

See here for the interactive Climate-based Critical Lands Protection Strategy and Ranking Tool Story Map!

The Peconic Estuary Partnership will be sharing this information with the municipalities within the Peconic Estuary watershed over the course 2020 and 2021.

Peconic Estuary Hardened Shoreline Mapping

With the help of GIS interns, PEP is completing a GIS mapping project to quantify the amount of hardened shoreline in the Estuary. The last survey was in Peconic Estuary Hardened Shoreline Mapping Report was completed in 2003. A final report of the recent study will be circulated when complete. 

Water Quality Monitoring Assessment

Peconic Estuary Partnership completed a Water Quality Monitoring Assessment with the assistance of CoastWise Partners, LLC.

The goal of this project was to create a Peconic Estuary Monitoring Strategy that will be relevant for all decision makers and to develop appropriate indicators of estuarine health, and ensure appropriate parameters are collected on a temporal and spatial scale to assess these indicators.

PEP held multiple workshops and Technical Advisory Committee meetings with our main water quality monitoring program partners to review current water quality monitoring programs, discuss gaps, the new CCMP goals, and develop strategies to improve monitoring programs and reporting to better track trends and progress in relation to CCMP implementation. CoastWise Partners helped guide the development of the updated monitoring strategy with the end goal of annual water quality reports.

In May of 2020, the Peconic Estuary Partnership Technical Advisory Committee recommended approval of the Peconic Estuary Water Quality Monitoring Strategy, a required element of the Peconic Estuary Partnership’s 2020 Comprehensive Conservation and Management Plan. The Management Committee and Policy Committee approved it in June 2020 and the final document is being formally approved by the EPA and incorporated into the CCMP.

The finalized Strategy includes a summary of existing water quality monitoring programs and an assessment of whether data collected by those programs can adequately track and detect changes in water quality needed to assess progress towards CCMP Goals. The Strategy also includes Next Steps to address gaps in data and/or information needed to fully assess progress towards CCMP Goals.

Click here for the PEP Water Quality Monitoring Strategy.

Water Quality Monitoring Collaborative

The PEP has developed a Peconic Estuary Monitoring Collaborative to help advise the completion of the Next Steps from 2020 through 2023 outlined in the PEP Water Quality Monitoring Strategy.

The Collaborative will function as a sub-committee of the Technical Advisory Committee (TAC) and is composed of main water quality monitoring programs in the Estuary- members of NYSDEC, USGS, Suffolk County, CCE,  and Academic monitoring groups.

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