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, shellfish harvesting, recreation, and tourism on the East End of Long Island are closely tied to the health of the Peconic Estuary. Changes in estuarine health can significantly impact the local economy. The expansion of land development and the increase in human population threaten water quality as well as the health of these economically important resources and habitats.

Poor water quality is directly linked to human activities on land, otherwise known as ‘non-point source pollution’. Non-point source pollution is caused by stormwater runoff or polluted ground water. which eventually seeps into the surrounding estuary waters and causes further contamination. In the Peconic Estuary, the primary sources of this pollution are wastewater from residential on-site septic systems and cesspools, fertilizers, and storm water runoff, in that order. Pathogens and toxic contaminants from non-point source pollution not only deteriorates the surrounding water quality, but can make fish and shellfish unsafe to eat.

One of the most serious issues affecting water quality in the Peconic Estuary is excessive nitrogen loading, which is known to subsequently cause harmful algae blooms, low dissolved oxygen, and degraded aquatic habitats. New and emerging contaminants from excessive nitrogen loading is posing a continued risk to ecological and human health in our watershed. Furthermore, plastic pollution in the aquatic environment are of increasing concern because of their persistence and effect on the environment, wildlife, and human health.

Understanding the connection between human actions on land and the health of the Peconic Estuary is crucial to its protection and restoration.

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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

Harmful Algal Bloom Management

Harmful algal blooms (HABs) have plagued the Peconic Estuary for decades, posing significant threats to public and environmental health. These blooms are increasingly frequent across various Suffolk County water bodies. Suffolk County’s marine waters are a crucial economic driver for Long Island, contributing to tourism, commerce, fishing, recreation, and more. Safe and attractive waters are essential for the success of these activities.

Current Actions

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 beaches and shellfisheries, thus impacting economic and recreational activities on the East End. At Peconic Estuary Partnership, we are working with our partners to reduce pathogen pollution caused by stormwater runoff and wastewater pollution.

Current Actions

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

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Toxic Contaminants in the Peconic Estuary

Plastic Pollution in the Peconic Estuary

PEP participates in regional Subwatershed Management efforts intended to reduce the loading of pesticides and herbicides. Some of these programs include our Agriculture Stewardship Plan, the initiatives of our PEP Citizens Advisory Committee, and the Homeowner Rewards Program.

PEP engages a variety of groups to participate in the Pesticide and Fertilize Elimination/Reduction Program. The groups could include golf courses, landscapers, municipal land owners, lawn care supply stores, environmental justice communities, and more.

PEP has also been working on various initiatives to reduce plastics in our waterways.

Current Actions


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