Department of Environmental Conservation

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Peconic Estuary Program

The Peconic Estuary system is located on the eastern end of Long Island, between the North and South Forks. The estuary includes more than 100 distinct bays, harbors, embayments and tributaries, including bays such as Flanders Bay, Great Peconic Bay, Little Peconic Bay, Shelter Island Sound, and Gardiners Bay.

Shows the borders of the Peconic Estuary System

The Peconic Estuary Program (PEP) (this link leaves the DEC website) is a cooperative effort between the state of New York State, Suffolk County, the United States Environmental Protection Agency (EPA), the scientific community, and the citizens of the Peconic Estuary watershed. In 2001 a Comprehensive Conservation and Management Plan (CCMP) (this link leaves the DEC website) was adopted and addresses issues noted below.

  • Nutrients
    Excess inputs of nitrogen have caused an imbalance in the estuary, which results in recurrent algae blooms and related drops in dissolved oxygen during the summer. This excess nitrogen is also suspected of contributing to a decline in eelgrass beds.
  • Habitat and Living Resource Losses
    As with most coastal areas around the country, the natural habitats of the Peconic Estuary and its watershed have been profoundly impacted by physical alterations like dredging, filling, clearing for agriculture and development.
  • Pathogens
    Organisms causing diseases in humans can be carried into the estuary where humans may be exposed by eating raw or partially cooked shellfish. Exposure to pathogens may also occur through direct contact with contaminated water or by swallowing it. A significant source of pathogens to the estuary is stormwater runoff which carries material from malfunctioning septic systems and animal waste.
  • Harmful Algal Blooms
    Harmful algal blooms (HABs) have plagued the Peconic Estuary since at least the mid 1980's, and the brown tide that occurred then was a main impetus for the creation of the Peconic Estuary Program. Although brown tides are no longer dominant, the Peconic Estuary experiences numerous other HABs annually, sometimes reaching world record concentrations.

Currently, the PEP is working on a revision to the 2001 CCMP, incorporating new environmental issues, management techniques, and scientific findings that have developed in the past 15 years. The revision will articulate the regional consensus about the most important environmental challenges facing the Peconic Estuary and the priority actions needed to address those challenges.