Protecting & Restoring Long Island's Peconic Bays

Water Quality

PEP is taking action to reduce nitrogen pollution, harmful algal blooms, pathogens, toxic contaminants, and plastics in the Estuary to support the well-being of people and wildlife.

Clean Waters for Ecosystem Health and Safe Recreation

Fishing, shellfishing, recreation, and tourism on the East End of Long Island are closely tied to the Peconic Estuary’s health, and changes in estuarine health can affect the local economy. Expansion of land development and the human population threatens to impair water quality and he health of these economically important resources and habitats.

Poor water quality is linked to people’s actions on land. In the Peconic Estuary, pollution tends to come from non-point sources like septic systems and residential and agricultural fertilizer, rather than point sources like sewage treatment plants. The pollution enters groundwater or surface waters, which carry it to the estuary.

One of the most serious issues affecting water quality in the Peconic Estuary is excess nitrogen loading, which can cause harmful algae blooms, low dissolved oxygen, and degraded aquatic habitats. Pathogens and toxic contaminants also contribute to water pollution in the Estuary, and can make fish and shellfish unsafe to eat. New and emerging contaminants pose a continued risk to ecological and human health in our watershed. Plastics in the aquatic environment are of increasing concern because of their persistence and effect on the environment, wildlife, and human health.

One of the most serious issues affecting water quality in the Peconic Estuary is excess nitrogen loading.

Poor water quality is tied to our actions on land. In the Peconic Estuary our primary pollution  source comes from many widely distributed sources– this is called non-point source pollution. Non-point source pollution is caused by the movement of water over the land surface (stormwater runoff) or through the ground- this water picks up natural and human-made pollutants, such as fertilizers, pesticides, motor oil, and human and animal waste, and  eventually ends up in lakes, rivers, wetlands, and coastal waters. The biggest sources of non-point source pollution in the Peconic Estuary is wastewater from residential on-site septic systems and cesspools. The second biggest source is fertilizer.

It is important that we understand the connection between human actions on land and the health of the Peconic Estuary.

Learn More!

Sources of Water Pollution in the Peconic Estuary

Long Island’s Aquifer 

Water Quality Updates

This figure shows the land area that contributes groundwater to the Peconic Estuary, and the amount of time it takes for this groundwater to reach the estuary. The groundwater contains natural and human-made pollutants.

Current Projects

Peconic Estuary Partnership provides program and project updates!

Search here for PEP Program Updates

Nitrogen Management>>

Harmful Algal Bloom Management>>>

Pathogen Management>>>

Toxic and Plastic Pollution Control>>>

Monitoring the Estuary’s Health>>>

Peconic Estuary Solute Transport Model

Peconic Estuary Partnership is working with the USGS to develop a Solute Transport Model for the Peconic Estuary Watershed. Here is a link to the USGS’s workplan for the Solute Transport Model. The USGS-PEP Solute Transport Modeling Project is developing a subregional solute transport model of the Peconic Estuary ground watershed to assess the time-varying discharge of nitrogen into fresh and coastal waters within the Peconic Estuary watershed. Once the model is complete it can then be applied to run a limited set of scenarios to estimate resulting nitrogen loading rates over time. These tools will provide valuable insights into how nitrogen discharge likely will change in response to nitrogen mitigation efforts within the watershed (such as changes to wastewater and fertilizer inputs to the groundwater) to guide local, state and regional management actions.

Nitrogen Load Reduction Assessment Project

PEP is working with Anchor QEA, LLC. to compile and assess the cost per pound of nitrogen reduction to groundwater for various nitrogen reduction best management practices (BMPs) currently being employed throughout the country.

The project will provide a decision-making tool to guide cost effective management scenarios to reduce nitrogen on a subwatershed basis in the Peconic Estuary. The project is planned to be complete in the Fall 2021.

Suffolk County’s Reclaim Our Water Initiative

Peconic Estuary Partnership fully supports the Suffolk County Reclaim Our Water Initiative to roll out the Septic Improvement Grant and Loan Program to incentivize the replacement of waste treatment systems that do not adequately reduce nitrogen pollution, such as septic systems and cesspools, with innovative/alternative onsite wastewater treatment systems (I/A OWTS). Peconic Estuary Partnership fully supports the 2020 Suffolk County Subwatersheds Wastewater Plan to comprehensively transition away from reliance on conventional cesspools and septic systems, which are the primary source of nitrogen pollution in the Peconic Estuary.

Long Island Nitrogen Action Plan

The Long Island Nitrogen Action Plan (LINAP) is a multiyear initiative to reduce nitrogen in Long Island's surface and ground waters by DEC, the Long Island Regional Planning Council (LIRPC), and Suffolk and Nassau counties, with input from multiple partners and stakeholders. PEP is committed to working with our partners to achieve the goals of LINAP. PEP's current projects are in alignment with LINAP goals and is conducting a social media campaign to educate the public and our stakeholders on the importance and relevance of LINAP.

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 Partnership 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 Partnership 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.

Reducing Fertilizer Use- Agricultural Stewardship

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. Click here to view the Agricultural Stewardship Plan. PEP continues to work with numerous partners (government agencies, non-profit organizations, academic institutions and private farmers) on  a Natural Resources Conservation Service’s Regional Conservation Partnership Program (RCPP), titled “Agricultural Stewardship in the Peconic Estuary Watershed” to provide technical assistance and financial resources to Suffolk County farmers within the federally-designated Peconic Estuary Watershed in New York to farmers to conduct nutrient management plans and integrated pest management plans to adapt best management practices, which will improve agricultural efficiencies and protect surface and groundwater quality, soil vitality and wildlife habitat.

Reducing Fertilizer Use- 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.

Harmful Algal Bloom Management

View of rust tide in the Peconic Estuary captured from a plane.

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 was heavily involved in the development of the Suffolk County Harmful Algal Bloom Action Plan, to aid in understanding HABs and to help focus future actions and management strategies. PEP will work with partners to implement the management recommendations in the plan.

Suffolk County Harmful Algal Bloom Action Plan

Pathogen Management

Learn more: Pathogen Pollution in the Peconic Estuary

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 Partnership 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. PEP is continuing to work with our partners to implement projects from these plans in the East End municipalities.

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. PEP works closely with the members of the Intermunicipal Agreement through the Peconic Estuary Protection Committee. Learn more here.

Peconic Estuary Program Monofilament Recycling Station along the Peconic River.
Peconic Estuary Partnership Monofilament Recycling Station along the Peconic River.

Toxic and Plastic Pollution Control

Learn more:

Toxic Contaminants in the Peconic Estuary

Plastic Pollution in the Peconic Estuary

PEP’s regional Subwatershed Management efforts, the Agriculture Stewardship Plan, the initiatives of the PEP Citizens Advisory Committee and the Homeowner Rewards Program  are all intended to reduce loadings of pesticides and herbicides. PEP engages a variety of groups (e.g., golf courses, landscapers, municipal land owners, lawn care supply stores, environmental justice communities, etc.) to participate in the Pesticide and Fertilize Elimination/Reduction Program. PEP has also been working on various initiatives to reduce plastics in our waterways.

Current Actions

Stop Throwing Out Pollutants

PEP promotes local and regional S.T.O.P (Stop Throwing Out Pollutants) days which are designed to provide area residents with a safe, environmentally sound method of disposal of the many hazardous materials found in the average home.

PEP and the Trash Free Waters Initiative

PEP is a partner in the Plastic Free Waters Partnership which is reducing the volume of trash entering U.S. waterways through a collaboration between many organizations around the country. The Peconic Estuary Partnership is continuing to support this collaboration across the public, higher education, nonprofit and private sectors with the goal of reducing plastic and microplastic debris in all waterbodies primarily in the New York/New Jersey region.  The partnership drives the latest research, policies, and education to implement strategies that protect our waters, health, and wildlife. The program focuses on: plastic bags, single-use beverage bottles, disposable take-out containers, microplastics, cigarette butts, straws, and balloons. Microbeads In 2015 Suffolk County banned micro-beads in personal care products, which went into effect on January 1st, 2018. The former Peconic Estuary Partnership Director, Alison Branco, was instrumental in gathering and assessing information about the environmental impacts of micro-beads and the logistics of banning their use, which contributed to the successful passage of the micro-bead ban bill. Plastic Bags PEP assisted Suffolk County in assessments of proposed legislation to reduce the use of single-use plastic bags. The final legislation establishes a 5 cent fee on single-use plastic bags, which went into effect in 2018.

Monofilament Fishing Line Collection and Recycling

PEP has installed monofilament fishing line receptacles at various location around the estuary to provide a place for fishermen to discard their excess fishing line and help combat marine plastic debris. PEP staff and volunteers will be responsible for collection and maintenance of the receptacles. During collection, we measure and record the receptacle weight and percentage filled to determine the amount of fishing line in each receptacle. Once collected, the fishing line will be sent to The Berkley Conservation Institute Pure Fishing, Inc. for recycling into tackle boxes, spools for line, fish habitats other products.

Here is a map of the sites where PEP and partner fishing line receptacles have been installed:

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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