Protecting & Restoring Long Island's Peconic Bays

Priority Issues in the Peconic Estuary

Learn what PEP is doing to address the priority issues in the Peconic Estuary!

Nitrogen Management>>

Harmful Algal Bloom Management>>>

Pathogen Management>>>

Habitat Restoration>>>

Climate Adaptation>>>

Toxic and Pollution Control>>>

Nitrogen Management

Reducing nitrogen loading to the Peconic Estuary, especially via groundwater, has been identified as a top priority for the Peconic Estuary Program, due to its far reaching impacts including harmful and toxic algal blooms, low dissolved oxygen and degraded aquatic habitats. The Peconic Estuary Program aims to reduce nitrogen loads by identifying sources of nitrogen on a subwatershed basis, and implementing management actions and projects to address these sources. PEP will also help to investigate emerging technologies as interim solutions to address existing groundwater contamination.

To implement cost effective management actions to reduce nitrogen loads to the estuary. PEP has invested a great deal of staff and committee time to coordinating with our partners in New York State, Suffolk County, US EPA, and the US Geological Survey to leverage related efforts with similar goals. PEP has been heavily involved in the following efforts.

PEP looks forward to collaborating with these partners to finally make progress on the most serious problem affecting water quality on Eastern Long Island.

Current Actions

Monitoring Nitrogen in the Peconic Estuary 
Monitoring of nitrogen in the Pecoinc Estuary is essential for understanding the the health of the Estuary. The Peconic Estuary Program supports both a year-round long-term periodic water sampling program conducted by the Suffolk County Department of Health Services (SCDHS) Office of Ecology, Bureau of Marine Resources and a continuous water sampling program conducted by the United States Geological Survey (USGS). These programs measure nitrogen levels in the water, as well as various other water quality indicators. Since 2003, the Peconic Estuary Program has also been monitoring the atmospheric deposition of nitrogen in the Peconic Estuary watershed, through our participation in the National Atmospheric Deposition Program. This data helps inform nitrogen management policies and goals.

Learn more about the Peconic Estuary Monitoring Programs here.

Improvements to Riverhead Sewage Treatment Plant
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.

Riverhead Purple Pipes Booklet

Reducing Fertilizer Use
A recent initiative to reduce pollution from agriculture is the Agricultural Stewardship Plan. The mission of the Agricultural Stewardship Program is to cooperatively develop a strategy to lower nutrient and pesticide loading associated with farming to the groundwater and surface waters of Suffolk County while maintaining a strong, viable agricultural industry.

Agricultural Stewardship Plan

Homeowner Rewards Program
Through the Homeowner Rewards Program  the PEP provides financial rewards for homeowners, in neighborhoods within the Peconic Estuary Watershed, who add raingardens, native plantings, and/or rain barrels to their properties. Simultaneously, the program educates the community about the benefits of raingardens, rain barrels, and native plants for nitrogen reduction.

Blue green algae bloom in freshwater.

Harmful Algal Bloom Management

Harmful algal blooms (HAB) have plagued the Peconic Estuary since at least the mid-1980’s and pose a public and environmental health threat. With an increasing frequency, we are seeing harmful algal blooms in various areas of our Suffolk County waterbodies. Suffolk County’s marine waters are a huge economic driver for Long Island in their contributions to tourism, commerce, fishing, recreation, and more. Safe and attractive waters play a key role in assuring the success of many of these activities.

Current Actions

HAB Action Plan
PEP will focus on reducing nitrogen loading, one of the primary causes of harmful algal blooms. Additionally PEP will be heavily involved in the Suffolk County 2016 effort to develop a county-wide Harmful Algal Bloom Research, Monitoring and Management Plan to aid in understanding HABs and to help focus future actions and management strategies.

Pathogen Management

Contamination of Peconic Estuary waters by bacteria and other pathogenic organisms may result in the closure of bathing beaches and the closure of shellfish beds for human consumption; thus impacting economic and recreational activities on the East End. The Peconic Estuary Program is working with its partners to reduce pathogen pollution from stormwater runoff and wastewater.

Current Actions

Subwatershed Management Plans
To decrease the amount of pollutants entering the water via stormwater we need to do our part to change what we do on land. PEP has worked to establish subwatershed management plans to address the pathogen loads to waterbodies troubled with pathogen pollution, and to date has created 12 subwatershed management plans.

These plans focuses on identifying cost‐effective structural and non‐structural practices to reduce overall pollutant loadings (i.e. bacteria, sediment, nutrients) and runoff volume to the subwatershed. Successful implementation of these plans is expected to help reduce stormwater runoff pollution and improve overall water quality conditions. This should in turn improve shellfish harvesting capacity, eelgrass habitat, and degraded marsh areas.

Map of watersheds chosen for assessment for the Peconic Estuary Subwatershed Management Plans.

Meetinghouse Creek, Riverhead

Hashamomuck Creek, Southold

Reeves Bay, Southampton

West Neck Bay, Shelter Island

Town and Jockey Creek, Southold

Goose Creek, Southold

Accabonac Harbor, East HamptonMap of watersheds chosen for assessment for the Peconic Estuary Subwatershed Management Plans.

Richmond Creek, Southold

Sebonac Creek Complex, Southampton

Dering Harbor, Shelter Island

North Sea Harbor, Southampton

Tanbark Creek, East Hampton

Intermunicipal Agreement
PEP established a collaboration of East End municipalities to share resources and work together on projects to reduce stormwater runoff, reduce pollution from septic system discharges, agricultural and residential fertilization, groundwater flows, illegal dumping, floatable debris and boat waste. Learn more here.

Habitat Restoration and Protection

PEP protects and restores priority habitats; including critical areas that support submerged aquatic vegetation, tidal wetlands and fish habitat, that are threatened by the alteration of the natural landscape from factors such as development, pollution and climate change.

Current Actions

PEP Habitat Restoration Plan
In 1997 the Peconic Estuary Program 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 and again in 2017. Over the years, the Peconic Estuary Program has completed projects to restore a variety of habitat types, including beaches/dunes, grasslands, diadromous fish habitat, eelgrass, and wetlands.

Peconic Estuary Program 2017 Habitat Restoration Plan

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 in 2009 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.

Peconic Estuary Program 2009 Eelgrass Management Plan

Eelgrass Management Plan: Implementation Progress Report 2016

Peconic Estuary Program 2015 Long-Term Eelgrass Monitoring Program Report

Land Protection
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 Program has developed a Critical Lands Protection Strategy (CLPS) that outlines land still available for development that also meet certain criteria used to determine land protection priorities. The Program shares this information with State and local agencies so that it can be used to make land acquisition decisions. PEP is currently updating the Critical Lands Protection strategy to account for climate change and rising seas (see Climate Change section).

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).

Peconic Estuary Program Critical Lands Protection Strategy

Climate Adaptation

PEP is working to ensure that climate change is considered in all PEP decision making, including the prioritization and selection of sites for restoration and acquisition. Maintaining and increasing living shorelines, updating the critical lands protection strategy, and educating stakeholders about the impacts of climate change on estuary resources will be priorities.

Current Actions

Peconic Estuary Climate Vulnerability Assessment
Currently PEP is completing a risk-based assessment, to account for future sea level rise, storm inundation and erosion potential. Based on the results of this assessment, a Climate Ready Action Plan will be developed to address prioritized climate change risks and vulnerabilities in the Peconic Estuary watershed and the Shinnecock Indian Nation. The intent of the Action Plan will be to identify methods to integrate climate change consideration into all phases of planning, design, and execution of the Peconic Estuary Program.


Considering Climate Change in the Critical Lands Protection Strategy
PEP is also completing an update to the Peconic Critical Lands Protection Strategy (CLPS), originally completed in 2004, to take into account climate related variables, specifically sea level rise, in order to update land acquisition priorities. This project will result in the protection and acquisition of lands the will continue to preserve and improve water and habitat quality in the face of rising sea levels and increased temperatures. It will allow for the natural inland migration of critical wetland habitats as sea level rises and preserve living shorelines in an environment where shoreline hardening is likely to become increasingly common. The information resulting from the new strategy will serve as an important tool for New York State, Suffolk County, and local agencies.


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