Health Services

Peconic Estuary Program FAQs

The Peconic Estuary is one of 28 estuaries in the National Estuary Program (NEP), administered by the United States Environmental Protection Agency (USEPA) under the auspices of Sec. 320 of the Clean Water Act to protect and preserve nationally significant estuaries which are threatened by pollution, development, or overuse. The Peconic Estuary was accepted into the program as an “estuary of national significance” in 1992.

Where is the Peconic Estuary and why is it important?
The Peconic Estuary is located between the North and South Forks of Long Island, and consists of over 100 harbors, embayments and tributaries which span more than 125,000 acres of land and 158,000 acres of surface water.

The Peconic Estuary provides important habitat, as well as spawning and nursery grounds, to a wide variety of marine organisms. Most notable are shellfish such as bay scallops and hard clams, and fish such as bay anchovy, Atlantic silverside, scup, (also called porgy), summer flounder (also called fluke), winter flounder, windowpane flounder, weakfish and blackfish. One of the most important underwater habitats of the Estuary is the meadows of eelgrass found along its eastern margin. These eelgrass beds provide food, shelter, and nursery grounds to many marine animals including shrimp, scallops and other bivalves, crabs, and fish.

Who is involved in the Peconic Estuary Program?
The Peconic Estuary Program (PEP) is sponsored by the USEPA, the New York State Department of Environmental Conservation (NYSDEC), and the Suffolk County Department of Health Services (SCDHS). The SCDHS, Office of Ecology operates the Program Office and provides the day-to-day management functions and the technical and administrative support to the program. Three additional committees within the Program, the Technical Advisory Committee, the Citizens Advisory Committee, and the Local Government Committee, are comprised of technical experts and federal, state, and local officials, as well as citizens. These stakeholders, collectively known as the PEP Management Conference, completed the final Comprehensive Conservation and Management Plan (CCMP), designed to protect and preserve the Peconic Estuary, in November of 2001.

What are the priority issues facing the Estuary?
The PEP Management Conference identified five priority management issues facing the estuary: brown tide, nutrient pollution, threats to habitat and living resources, pathogen contamination, and toxic chemicals. These five priority management issues, together with the need for public education and outreach, financing, and a framework for the long-term management of the estuary, form the basis for the actions included in the Peconic Estuary Program’s Comprehensive Conservation and Management Plan.

What happens now that the Comprehensive Conservation and Management Plan (CCMP) has been adopted?
The existing Peconic Estuary Program Management Conference structure remains intact. The Local Government Committee, Technical Advisory Committee, and Citizens Advisory Committee are integral to the long-term management process. The Program office has continued its management, coordination, and administrative functions, as they are applicable to post-CCMP management, and as resources allow. Collectively, the PEP partners are working to implement the CCMP.

How much has been spent on planning and implementing the Comprehensive Conservation and Management Plan?
To date approximately $10 million in USEPA funding, with significant Suffolk County and NYSDEC match, has been provided for the implementation of the management plan and associated research and monitoring activities. Over 120 priority demonstration and implementation projects have been funded using federal and state funds totaling over $20.2 million. Even more significantly, with state and local funding sources such as the New York State Clean Water/Clean Air Bond Act and the Suffolk County ¼% Sales Tax, tens of millions of dollars will potentially be committed to the Peconic Estuary over the next decade.

What are a few of the Peconic Estuary Program’s achievements and initiatives?
  • Adoption of a nitrogen guideline and a point source nitrogen freeze for the western estuary
  • Adoption of a water quality preservation policy for the eastern estuary
  • Development of a preliminary submerged aquatic vegetation and management strategy, including a long-term monitoring, restoration trials to develop survival criteria, and integration with water quality monitoring and modeling
  • Development of a Pathogens Total Maximum Daily Load (TMDL) for 21 water bodies listed as impaired on New York State’s 303(d) list
  • Development of a Nitrogen TMDL for selected water bodies in the western estuary
  • Creation of the PEP Critical Lands Protection Plan, prioritizing the preservation of lands available for development
  • Preparation of an Environmental Indicators Report detailing the relative health and stresses on the water body. The report focused on key parameters including Brown Tide, nutrients, habitat and living resources, pathogens, toxic substances and land management issues, and concluded that the estuary is in overall good condition although significantly impacted in the more densely developed western bays and tributaries.
  • Support for a PEP State of the Bays Science Conference that was held in April 2005 and featured presentations by 18 scientists
  • Implementation of subwatershed management plans for Reeves Bay, Hashamomuck Pond, West Neck Bay and Meetinghouse Creek.  Contracts for six additional watershed management plans have been completed for Town and Jockey Creeks, Goose Creek, Richmond Creek, Acabonac Harbor, Sebonac Creek Complex and Dering Harbor.
  • Developed GIS layers of land cover, impervious surfaces, eelgrass beds, hardened shoreline and protected lands.
  • Supported a large scale 2.7 million dollar scallop restoration project conducted by Cornell Cooperative Extension and Long island University, to jump start Peconic Bay scallop populations
  • State-of-the-art technical characterizations and management tools, including sediment nutrient flux and surface water modeling studies
  • Implementation of an early detection rapid response monitoring and volunteer eradication program for Ludwigia peploides (water primrose) from the freshwater Peconic River
  • Installation of a rock ramp fish ladder on the Peconic River at Grangebel Park in Riverhead, to facilitate alewives access to the freshwater portion of the river
  • Participation in the Suffolk County Shellfish Aquaculture Lease Program for Peconic Bay and Gardiners Bay
  • Secured funding for research into the causes and effects of harmful algal blooms in the estuary caused by the organism Cochlodinium polykrikoides
  • To increase public education and outreach, a website has been created (link below), and an electronic newsletter, "Peconic Press", that provides updates on current topics affecting the estuary, is issued quarterly.
How can I get a copy of the Peconic Estuary Program’s Comprehensive Conservation and Management Plan (CCMP)?
A copy of the final CCMP can be obtained from the PEP Program Office (see below), or by visiting the PEP website: http://www.peconicestuary.org/

What other reports have been written for the Peconic Estuary Program?
For copies of reports, contact the PEP Program Office:

Peconic Estuary Program
Suffolk County Department of Health Services 
Office of Ecology 
360 Yaphank Ave. Suite 2B 
Yaphank, NY 11980 
Tel: (631) 852-5750 
Fax: (631) 852-5812