Guiding The Next Decade in the Peconics

PEP’s New Management Plan Faces Threats to the Estuary

The Peconic Estuary was named an “Estuary of National Significance” way back in 1992, part of a decades-long effort to protect the vibrant ecosystem that calls the space between the twin forks home.

The Peconic Estuary Partnership (PEP) has been working the past couple years to update its Comprehensive Conservation Management Plan, using 2020 as a jumping-off point for the next ten years of protecting the Peconics.

The next decade will prove to be crucial to the future of the estuary, as development pressures, rising sea levels, declining water quality and the impact of climate change on the ecosystem all pose severe threats.

“With the completion of The Peconic Estuary Partnership’s management plan, we now have a road map for combating the many threats facing the Peconic watershed,” said New York Senator Chuck Schumer. “With ever increasing nitrogen levels, annual algal blooms, and climate change, it is imperative that we invest in the research to fully assess these threats to our coastal areas. We must then follow the science and build sound policy at the federal, state, and local level to preserve our ecological resources for future generations.”

The new plan was unveiled in late October, and it focuses on four primary goals — building strong partnerships, resilient communities and a healthy ecosystem and ensuring clean water in the estuary.

To meet those goals, the plan lays out eight new objectives and 35 specific actions.

According to the authors of the plan, “some of the critical challenges we face are the impacts of climate change such as sea level rise, more frequent and more intense storms, and how changing weather patterns will affect habitat and living resources, water quality, and watershed management practices.”

Other issues include “hardened shorelines — seawalls, bulkheads, and other shoreline structures are constructed at a rapid pace, eliminating vital habitats for many species; land development pressuring the ecosystem and habitat connectivity, affecting terrestrial, aquatic, and avian species; nitrogen pollution from septic systems and cesspools, and residential and agricultural fertilizer; pollutants from activities on land such as excess nutrients, pathogens, pharmaceutical compounds and toxic contaminants such as pesticides and per- and polyflouroalkyl substances (PFAS).”

Ecosystem challenges have “threatened Bay Scallop populations, declining eelgrass beds—which serve as nurseries for scallops and fish—have diminished dramatically and are vulnerable to further decline with climate change, and harmful algae blooms are more frequent,” according to the authors of the plan.

“As a coastal community on Long Island, we share the same water and the same habitats, and as a result, we must work together to address the same environmental issues,” said the plans’ authors. “It is our partnerships that bring positive change and our partnerships that will usher in the next decade of clean water and healthy habitats. PEP strives to increase community awareness and the inclusion of all of our communities, ensuring people know of the challenges we face while helping people to understand what they can do to support Estuary health. Our partnership is our greatest tool to help us achieve the goals and actions outlined in the 2020 CCMP. We welcome the next decade of working together to follow the plan we built together for the protection and restoration of our Estuary.”

The critical challenges facing the Peconic Estuary, as outlined in the new management plan.

“Since 2000, EPA has invested approximately $12 million to support the preservation of the Peconic Estuary,” said EPA Regional Administrator Pete Lopez. “The restoration of this critical ecological resource and the protection of its water quality are important for the aquatic life, ecosystem and communities who utilize the estuary for commercial and recreational purposes. This updated Comprehensive Conservation and Management Plan demonstrates our commitment to build on the progress of the Peconic Estuary Partnership and further revitalize the economic health and vitality of this important watershed.”

The first goal, building strong partnerships, involves engaging the community in protecting the estuary, encouraging people to understand why the health of the Peconic Estuary is important to them, how their actions impact the estuary, and what they can do to improve the estuary’s health. 

This goal includes empowering local communities to support the estuary, through actions ranging from expanded citizen science programs to incorporating environmental justice goals into PEP’s work. 

Building on the formation of the strong partnerships, the second goal, creation of resilient communities, involves engaging neighborhoods in the fight against climate change.

 The Peconic Estuary Partnership hopes to further this goal by helping local governments conserve and acquire land to protect habitat and promote climate resiliency, and to develop strategies to mitigate the impact of climate change. 

They also plan to work to understand the roles of seagrass beds and wetlands in coastal resilience, and to develop pilot projects to gather data on carbon sequestration by wetlands, eelgrass and kelp, a so-called “blue carbon” initiative.

PEP also plans to be a partner in ocean acidification research conduced by the New York State Department of Environmental Conservation, Stony Brook University, Suffolk County and the U.S. Geological Survey, and to collaborate with the Shinnecock Indian Nation on its Climate Ready Assessment and Action Plan.

Much is currently being done with regard to clean water initiatives in the Peconic Estuary watershed, and PEP’s third goal involves engaging with much of the work already underway. PEP plans to play a role in identifying and protecting clean water areas, to help to monitor and reduce nutrient pollution in the estuary, and to augment existing efforts to upgrade septic systems in the watershed. They also plan to collect data on harmful algae blooms, in partnership with New York Sea Grant, the DEC, Suffolk County and Stony Brook University. They also plan to monitor and work to stop sources of toxic contaminants entering the estuary.

The final goal of the CCMP, of ensuring a healthy ecosystem with abundant, diverse wildlife,  includes protecting and restoring eelgrass beds; restoring habitat, including fish ladders, for diadromous fish like alewives; prioritizing wetland restoration projects, implementing living shoreline projects and protecting the habitat of important species like the river otter, diamondback terrapin and horseshoe crab, and encouraging the creation of shellfish spawner sanctuaries. 

They also plan to be involved in spacial planning of the use of resources in the estuary — an issue that has come to the fore in recent years as recreational boaters have come into conflict with shellfish growers here. 

“For nearly three decades the PEP and its guiding management plan have made a measurable difference in protecting and restoring the health of the Peconic Bay Estuary, and the regional economy it supports,” said Bob DeLuca, President and CEO of Group for the East End. “By bringing diverse interests together and pursuing a regional conservation and management strategy, the PEP has shown the positive impact that can occur when scientific knowledge is paired with community partnership.”

The full plan is online at

— BY

Beth Young

Beth Young built her first boat out of driftwood tied together with phragmites behind her family’s apartment above the old Mill Creek Inn in Southold. Nowadays, she spends most of her time kayaking, learning about shellfish, writing newspaper stories, trying to sail a Sunfish, and watching the way the bay changes from day to day. You can send her a message at

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