Protecting & Restoring Long Island's Peconic Bays

Clean Waters

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.

View looking across Flanders Bay. Credit: Peter Ormand

Fishing, shelfishing, 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>>>

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.


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