Protecting & Restoring Long Island's Peconic Bays

PEP: Making significant change

The PEP is a comprehensive, regional, watershed-based program, the perfect mechanism to implement programs and initiatives that can result in measurable water quality improvements.

Established in 1987 under the Clean Water Act, the National Estuary Program (NEP) operates through partnerships with EPA and other public and private sector entities to “identify, restore, and protect nationally significant estuaries of the United States.” The NEP hosts locally-based, stakeholder driven programs that are non-regulatory, collaborative initiatives working with the community to craft and implement action plans to solve environmental problems at the watershed level.

Image of the National Estuary Program Map

There are 28 National Estuary Programs across the continental United States and Puerto Rico. In 1992, the Peconic Estuary became the 20th estuary in the nation to receive the designation as an “Estuary of National Significance” by the U.S. Environmental Protection Agency (EPA).

Established in 1992, the Peconic Estuary Program (PEP) integrates environmental and economic issues for all east-end towns and has brought over $13 million in federal grant funding to the Peconic Estuary watershed.

One major aspect of the Peconic Estuary Program’s leadership is its effective use of funds provided by EPA to leverage additional support.

The NEP’s exemplify efficient and effective governance.  For every one dollar provided by the federal government, $19 is contributed by NEP’s non-federal partners. For example, the Peconic Estuary Program used its annual NEP grant to secure an additional $22 million in leveraged resources from public and private funders. The resources were used to help address Peconic Estuary’s priority problems, including: nutrients, pathogens, toxic chemicals, harmful algae, loss of critical habitats and natural resource threats.

Check out the Priority Issues in the Peconic Estuary page to view projects PEP is moving forward!

The Value of PEP to our Stakeholders>>>
Accomplishments Over 25 Years>>>

The Value of PEP to our Stakeholders

The PEP provides leadership and coordination to restore and maintain the water quality and ecological integrity of the Peconic Bays and the surrounding watershed. The work of the PEP protects water quality and in turn improves the condition of shellfish, fish, and wildlife. These efforts are critical to preserving the quality of life for all Suffolk County residents and promote local and regional economies that increasingly rely on tourism, recreational fishing, boating, and other water-dependent industries.

The PEP is a comprehensive, regional, watershed-based program, the perfect mechanism to implement programs and initiatives that can result in measurable water quality improvements. PEP’s watershed management plan, or Comprehensive Conservation Management Plan, represents a regional consensus on the water quality improvement action agenda. As a result, the PEP helps to shape other regional water quality projects and programs and increases Federal and State funding attention on those priority actions. Stakeholder participation in this regional water quality planning effort is beneficial to all as it incorporates the local interests very effectively into a regional strategy.

Accomplishments Over 25 Years

Water Quality Improvements

The Full Story

Nitrogen Management has always been an important part of the Peconic Estuary Program's Strategy to protect and restore water quality in the Peconic Estuary.  Initially focused on point sources and direct discharges, many important steps were taken to reduce nitrogen loading to the Peconic Estuary including the establishment of the Vessel Waste No-Discharge Zone in 2002 and The PEP has supported the establishment of the Suffolk County Fertilizer Reduction Law in 2007 in an effort to reduce nitrogen loads from fertilizer applications.

Additionally, in 2007 NY State developed a nitrogen pollutant load limit for the Peconic Estuary called the Total Maximum Daily Load for Nitrogen for the Peconic Estuary . This pollutant load limit, Total Maximum Daily Load (TMDL), for Nitrogen is a pollutant diet that the waterbody must comply with to address the poor water quality in the western Peconic Estuary.  The TMDL determined the amount of pollutant load that can be discharged from point sources discharges (such as outfall pipes) and pollution sources that are diffuse (termed “non-point sources”) to achieve or maintain water quality standards. The introduction of  Nitrogen TMDL supported the major upgrades to Sewage Treatment Plants within the Estuary. The Peconic Estuary Program was influential in moving the 2016 Riverhead Sewage Treatment Plant upgrade and reuse project forward to reuse highly-treated wastewater to irrigate the Indian Island Golf Course.

Furthermore, PEP has developed 12 Subwatershed Management Plans for the Peconic Estuary that identify cost‑effective strategies to help reduce pathogen and stormwater runoff pollution and improve water quality (2006- Developed 5 Subwatershed Management Plans, 2013- Developed 7 Subwatershed Management Plans). Many of the Towns have successfully implemented projects identified in the Subwatershed Management Plans! To improve collaboration on stormwater pollution mitigation, in 2015 PEP and the East End municipalities entered into an Intermunicipal Agreement to reduce stormwater runoff and pollution from septic system discharges, agricultural and residential fertilizer, groundwater flows, illegal dumping, floatable debris, and boat waste.

The PEP has fostered sustainable practices in backyards on the East End, the Homeowner Rewards Program has helped 32 property owners since 2014 complete sustainable upgrades to their yards by installing native plant gardens, rain gardens or rain barrels.  To date  56,123 square feet of native plants garden, 3,300 square feet of rain garden, and 46 rain barrels have been installed through the program. Reducing fertilizer and pesticide use and reducing water use.

Vessel Waste No-Discharge Zone in 2002

The entire Peconic Estuary was designated as a federally recognized Vessel Waste No Discharge Zone (NDZ) in 2002 in order to help protect our shellfish beds and keep our waters safe and clean for swimming and recreation. In a NDZ, treated and untreated discharges from marine toilets are prohibited. To ensure compliance with the NDZ, boaters must modify their “heads” to prevent discharges.

Suffolk County Fertilizer Reduction Law in 2007

The PEP has supported the establishment of the Suffolk County Fertilizer Reduction Law in 2007 in an effort to reduce nitrogen loads from fertilizer applications.

Total Maximum Daily Load for Nitrogen for the Peconic Estuary in 2007

In 2007 NY State developed a nitrogen pollutant load limit for the Peconic Estuary called the Total Maximum Daily Load for Nitrogen for the Peconic Estuary . This pollutant load limit, Total Maximum Daily Load (TMDL), for Nitrogen is a pollutant diet that the waterbody must comply with to address the poor water quality in the western Peconic Estuary.  The TMDL determined the amount of pollutant load that can be discharged from point sources discharges (such as outfall pipes) and pollution sources that are diffuse (termed “non-point sources”) to achieve or maintain water quality standards. The introduction of  Nitrogen TMDL supported the major upgrades to Sewage Treatment Plants within the Estuary.

12 subwatershed plans for the Peconic Estuary in 2006 and 2013

PEP has developed 12 Subwatershed Management Plans for the Peconic Estuary that identify cost‑effective strategies to help reduce pathogen and stormwater runoff pollution and improve water quality (2006- Developed 5 Subwatershed Management Plans, 2013- Developed 7 Subwatershed Management Plans). Many of the Towns have successfully implemented projects identified in the Subwatershed Management Plans!

The Homeowner Rewards Program in 2014

The PEP has fostered sustainable practices in backyards on the East End, the Homeowner Rewards Program has helped 32 property owners since 2014 complete sustainable upgrades to their yards by installing native plant gardens, rain gardens or rain barrels.  To date  56,123 square feet of native plants garden, 3,300 square feet of rain garden, and 46 rain barrels have been installed through the program. Reducing fertilizer and pesticide use and reducing water use.

The Peconic Estuary Intermunicipal Agreement in 2015

To improve collaboration on stormwater pollution mitigation, in 2015 PEP and the East End municipalities entered into an Intermunicipal Agreement to reduce stormwater runoff and pollution from septic system discharges, agricultural and residential fertilizer, groundwater flows, illegal dumping, floatable debris, and boat waste.

Upgrades and reuse project at the Riverhead Sewage Treatment Plant in 2016

The Peconic Estuary Program was influential in moving the 2016 Riverhead Sewage Treatment Plant upgrade and reuse project forward to reuse highly-treated wastewater to irrigate the Indian Island Golf Course.

In summer of 2016, after nearly 20 years of planning, the Riverhead Sewer District celebrated the completion of its upgrade and the First-on-Long-Island “Water Resource Recovery Facility”. The Riverhead Town Sewage Treatment Plant will reuse highly-treated wastewater to irrigate the Indian Island Golf Course. This will divert approximately 1.4 tons of nitrogen per year from entering the Peconic Estuary via the Riverhead Sewage Treatment plant outfall pipe, and the improved treatment technology at the plant will help to further reduce the nitrogen load to the Estuary. Additionally, this will save an estimated 350,000 gallons of water each summer day because now instead of using water from drinking water supply wells to irrigate the course golf course, the highly-treated wastewater will be used instead. Using the treated wastewater will also reduce the amount of fertilizer needed at the golf course, thereby reducing the nitrogen load contributed by surface water runoff. View & Download the Riverhead Purple Pipes Booklet

 

Habitat Improvements

The Full Story

Cited as one of the “Last great places in the Western Hemisphere,” the Peconic Estuary contains a rich mosaic of natural communities, all of which are important to the ecology and productivity of this ecosystem. There is a larger percentage of undisturbed habitats and a greater diversity of natural communities within the Peconic Estuary watershed, on a per unit area basis, than anywhere else in the coastal zone of New York State. The Peconic Estuary Program has worked with our partners to protect and restore habitats in the Peconic Estuary watershed and protect the ecosystem services they provide.

The Peconic Estuary Program Habitat Restoration Plan prioritizes habitat restoration projects and since 2000 27 habitat restoration projects have been completed. Completed projects include 2 beach restorations, 2 shorebird habitat restorations, 7 wetland restoration projects, 2 phragmites control project, 1 grassland restoration project, 3 water quality improvement projects, 2 diadromous fish habitat restoration projects, 6 shellfish restoration projects, and 2 eelgrass restoration projects.  See the Habitat Restoration Map to view information on completed and ongoing projects.

Monitoring data collected and reported under the Peconic Estuary Program Long-Term Eelgrass Monitoring Program indicated that the Bullhead Bay eelgrass bed, the western-most bed in the Peconic Estuary, was in severe decline and was being impacted greatly by physical disturbances, especially shellfish harvesting. This information was presented to the Southampton Trustees, who then designated the bed as an eelgrass sanctuary to prohibit shellfishing within its boundaries in 2009.

To promote shellfish restoration in 2013, the Hard Clam and American Oyster Enhancement and Restoration in Lake Montauk project was completed which was funded in part by the Peconic Estuary Program. The project involved growing and seeding one million clams and 500,000 oysters into Lake Montauk during 2012 and 2013.

The PEP supported the completion of the Long Island Tidal Wetlands Trends Analysis in 2015 which measured wetlands loss and changes in marsh condition within the Long Island Sound, Peconic, and South Shore estuaries including all or parts of Westchester, Bronx, Queens, Nassau, and Suffolk Counties. The results of this project are used by environmental managers, conservation advocates and elected officials across a variety of regulatory agencies, environmental organizations, and governments.

In support of improving populations of diadromous fish to date the Peconic Estuary Program has helped to open up 35 acres of freshwater habitat on the Peconic River with the completion of the Grangebel Park Natural Fishway in 2010 and Edwards Avenue fish passage in 2016.

To move forward priority habitat restoration projects, PEP has developed 9 Conceptual Designs to assist Towns in taking steps towards habitat restoration.  a conceptual design for Shell Beach Native Vegetation Restoration was completed in 2012, and a conceptual design for Napeague Harbor Circulation Enhancement was completed in 2013, additionally in 2013 PEP funded 3 conceptual designs for fish passage at Forge Road Dam, Ligonee Brook, and Moore’s Drain. In 2019 conceptual habitat restoration designs have been developed for the following 4 identified priority sites: Southold: Narrow River Road Wetland Restoration, Southampton: Iron Point Wetland Restoration, East Hampton: Lake Montauk Alewife Access and Habitat Enhancement and Riverhead: Meetinghouse Creek Main Road Wetland Construction/Restoration.

In 2019 the Widows Hole Preserve Living Shoreline Project was completed in Greenport with Peconic Land Trust and Cornell Cooperative Extension of Suffolk County.  This is the first living shoreline project in the Peconic Estuary.

In 2019 the Seagrass Bio-optical Model was 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

27 Completed Projects since 2000

The Peconic Estuary Program Habitat Restoration Plan prioritizes habitat restoration projects and since 2000 27 habitat restoration projects have been completed. Completed projects include 2 beach restorations, 2 shorebird habitat restorations, 7 wetland restoration projects, 2 phragmites control project, 1 grassland restoration project, 3 water quality improvement projects, 2 diadromous fish habitat restoration projects, 6 shellfish restoration projects, and 2 eelgrass restoration projects.  See the Habitat Restoration Map to view information on completed and ongoing projects.

Bullhead Bay Eelgrass Sanctuary in 2009

Monitoring data collected and reported under the Peconic Estuary Program Long-Term Eelgrass Monitoring Program indicated that the Bullhead Bay eelgrass bed, the western-most bed in the Peconic Estuary, was in severe decline and was being impacted greatly by physical disturbances, especially shellfish harvesting. This information was presented to the Southampton Trustees, who then designated the bed as an eelgrass sanctuary to prohibit shellfishing within its boundaries in 2009.

Shellfish Restoration Efforts in 2013

To promote shellfish restoration in 2013, the Hard Clam and American Oyster Enhancement and Restoration in Lake Montauk project was completed which was funded in part by the Peconic Estuary Program. The project involved growing and seeding one million clams and 500,000 oysters into Lake Montauk during 2012 and 2013.

35 Acres of Freshwater Habitat Opened on the Peconic River

In support of improving populations of diadromous fish to date the Peconic Estuary Program has helped to open up 35 acres of freshwater habitat on the Peconic River with the completion of the Grangebel Park Natural Fishway in 2010 and Edwards Avenue fish passage in 2016.

Long Island Tidal Wetlands Trends Analysis in 2015

The PEP supported the completion of the Long Island Tidal Wetlands Trends Analysis in 2015 which measured wetlands loss and changes in marsh condition within the Long Island Sound, Peconic, and South Shore estuaries including all or parts of Westchester, Bronx, Queens, Nassau, and Suffolk Counties. The results of this project are used by environmental managers, conservation advocates and elected officials across a variety of regulatory agencies, environmental organizations, and governments.

9 Habitat Designs Completed as of 2019

To move forward priority habitat restoration projects, PEP has developed 9 Conceptual Designs to assist Towns in taking steps towards habitat restoration.  a conceptual design for Shell Beach Native Vegetation Restoration was completed in 2012, and a conceptual design for Napeague Harbor Circulation Enhancement was completed in 2013, additionally in 2013 PEP funded 3 conceptual designs for fish passage at Forge Road Dam, Ligonee Brook, and Moore’s Drain. In 2019 conceptual habitat restoration designs have been developed for the following 4 identified priority sites: Southold: Narrow River Road Wetland Restoration, Southampton: Iron Point Wetland Restoration, East Hampton: Lake Montauk Alewife Access and Habitat Enhancement and Riverhead: Meetinghouse Creek Main Road Wetland Construction/Restoration.

1st Peconic Estuary Living Shoreline Project Completed in 2019

In 2019 the Widows Hole Preserve Living Shoreline Project was completed in Greenport with Peconic Land Trust and Cornell Cooperative Extension of Suffolk County.  This is the first living shoreline project in the Peconic Estuary.

Seagrass Restoration Tool in 2019

In 2019 the Seagrass Bio-optical Model was 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.

 

Land Protection

The Full Story

The Peconic Estuary Program developed the Critical Lands Protection Strategy in 2004 which supported the establishment and implementation of the Community Preservation Fund to protect land from development and preserve the health of the Peconic Estuary. The Community Preservation Fund was established in 1998 and managed by the East End towns for the protection of farmland, open space, and community character. The CPF is a one-time real estate transfer tax of 2% on improved or vacant property. In 2016, voters extended the CPF to 2050 and approved an amendment allowing towns to invest up to 20% of the funds in water quality improvement projects. With an agreement that 10% of that 20% could be allocated to the Peconic Estuary Program.

This coordinated effort resulted in a total of 4,045 acres of land protected in the watershed to date.

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. The lands within the watershed were evaluation and prioritized considering climate change impacts.

The Community Preservation Fund in 1998

The Community Preservation Fund was established in 1998. The CPF is a public program managed by the East End towns for the protection of farmland, open space, and community character. The CPF is a one-time real estate transfer tax of 2% on improved or vacant property.

In 2016, voters extended the CPF to 2050 and approved an amendment allowing towns to invest up to 20% of the funds in water quality improvement projects. With an agreement that 10% of that 20% could be allocated to the Peconic Estuary Program.

The Critical Lands Protection Strategy in 2004

The Peconic Estuary Program developed the Critical Lands Protection Strategy in 2004 which supported the establishment and implementation of the Community Preservation Fund to protect land from development and preserve the health of the Peconic Estuary. This coordinated effort resulted in a total of 4,045 acres of land protected in the watershed to date.

The Updated Critical Lands Protection Strategy in 2019

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. The lands within the watershed were evaluation and prioritized considering climate change impacts.

 

Climate Adaptation

The Full Story

The Peconic Estuary faces numerous pressures including development, habitat loss, and nutrient loading. Climate change poses another set of challenges; among them are sea level rise (SLR), more frequent and more intense storms, and changing weather patterns—as well as the human responses to them. All have the potential to further degrade water and habitat quality and lead to greater habitat loss and fragmentation. To address climate issues, in 2016 PEP embarked on a Climate Ready Assessment (CRA) Project to incorporate climate change into an updated CLPS, to conduct a risk-based climate change vulnerability assessment, and to develop an adaptation action plan consistent with USEPA’s Climate Ready Estuaries Program.

In 2019, The Peconic Estuary Program created a guide for the municipalities and resources managers in the Peconic Estuary and the Shinnecock Indian Nation to adapt to the impacts of climate change.

Climate Ready Action Plan in 2019

In 2016 PEP embarked on a Climate Ready Assessment (CRA) Project to incorporate climate change into an updated CLPS, to conduct a risk-based climate change vulnerability assessment, and to develop an adaptation action plan consistent with USEPA’s Climate Ready Estuaries Program.

In 2019, The Peconic Estuary Program created a guide for the municipalities and resources managers in the Peconic Estuary and the Shinnecock Indian Nation to adapt to the impacts of climate change.

 

Monitoring the Estuary’s Health

The Full Story

Since PEP’s inception the program has supported the robust surface water quality monitoring in the Peconic Estuary run by the Suffolk County Department of Health Services Bureau of Marine Resources. Through PEP funding, the water quality monitoring program conducted by the Suffolk County Department of Health Services (SCDHS) Office of Ecology includes monthly monitoring at 38 Peconic surface water quality stations throughout the year, periodic monitoring of 26 point source and stream stations.

To compliment the Suffolk County Water Quality Monitoring Program, in 2012 the PEP established 2 water quality monitoring stations in the Peconic Estuary which are maintained by the United States Geological Survey and provide continuous information on the state of the water quality in the estuary.

To keep a pulse on the pollution impacting the Estuary from the atmosphere, since 2003 the Peconic Estuary Program has been monitoring the atmospheric deposition of nitrogen in the Peconic Estuary watershed, through our participation in the National Atmospheric Deposition Program.

Since 1997, PEP has supported Cornell Cooperative Extension of Suffolk County Long-term monitoring of eelgrass survival and measurements of seagrass extent every year.

In addition to supporting the above monitoring programs, the PEP provides many opportunities for citizens to get involved by attending an educational event or volunteering through our ongoing citizen science programs. PEP coordinates 4 citizen programs that focus on collecting information on Horseshoe Crabs, Alewife, and TerrapinsPEP's Fishing Line Recycling Program  is another helpful way that the public can help the PEP reduce excess fishing line from harming marine life and help the PEP monitor the areas where the fishing line receptacles are or are still needed.

Surface Water Quality Monitoring since 1977

Since PEP’s inception the program has supported the robust surface water quality monitoring in the Peconic Estuary run by the Suffolk County Department of Health Services Bureau of Marine Resources. Through PEP funding, the water quality monitoring program conducted by the Suffolk County Department of Health Services (SCDHS) Office of Ecology includes monthly monitoring at 38 Peconic surface water quality stations throughout the year, periodic monitoring of 26 point source and stream stations.

Eelgrass Monitoring since 1997

Since 1997, PEP has supported Cornell Cooperative Extension of Suffolk County Long-term monitoring of eelgrass survival and measurements of seagrass extent every year.

Atmospheric Deposition Monitoring since 2003

To keep a pulse on the pollution impacting the Estuary from the atmosphere, since 2003 the Peconic Estuary Program has been monitoring the atmospheric deposition of nitrogen in the Peconic Estuary watershed, through our participation in the National Atmospheric Deposition Program.

Continuous Water Quality Monitoring since 2012

To compliment the Suffolk County Water Quality Monitoring Program, in 2012 the PEP established 2 water quality monitoring stations in the Peconic Estuary which are maintained by the United States Geological Survey and provide continuous information on the state of the water quality in the estuary.

4 Citizen Science Programs

In addition to supporting the above monitoring programs, the PEP provides many opportunities for citizens to get involved by attending an educational event or volunteering through our ongoing citizen science programs. PEP coordinates 4 citizen programs that focus on collecting information on Horseshoe Crabs, Alewife, and TerrapinsPEP's Fishing Line Recycling Program  is another helpful way that the public can help the PEP reduce excess fishing line from harming marine life and help the PEP monitor the areas where the fishing line receptacles are or are still needed.

 

Connect with Us

Sign up for News, Events and Information straight to your inbox.