Protecting & Restoring Long Island's Peconic Bays

Climate Change

PEP will lead scientifically informed, proactive efforts by local communities that can reduce the negative impacts of climate change.

Resilient Communities Prepared for Climate Change

House on stilts on the shore of the Peconic Estuary.

The influence of climate change on the Peconic Estuary and the communities around it will grow profoundly far into the future. Scientifically informed, proactive efforts can reduce the negative impacts.

Projected changes in precipitation patterns, particularly increases in extreme rain events, will likely cause greater runoff of nutrients and other pollutants from land into the Estuary and may also increase atmospheric deposition of pollutants. Rising sea levels are expected to result in increasingly frequent inundation of drinking water wells and septic systems on coastal properties, leading to more nitrogen and pathogens entering groundwater, surface waters, and the Estuary. In turn, greater nitrogen loading of the Peconic Estuary can be expected to result in more frequent harmful algal blooms, reduced water clarity, and a general degradation of coastal habitats. Excessive pathogens may lead to more frequent closures of bathing beaches and shellfish harvesting areas, while herbicides and pesticides are increasingly being linked to losses of seagrasses and other marine habitats that serve as important feeding and nursery areas for recreationally and commercially important fish species.

As temperatures increase, sea levels rise (SLR), and precipitation occurs with increasing intensity, estuarine species and habitats may move or change. Where there is significant coastal development and shoreline hardening, important habitats such as salt marshes could be blocked from migrating landward as sea levels rise. Changes in air and water temperatures may lead to shifts in the relative abundance of fish and other estuarine species. Species once thought to be more southerly or warm-adapted may become more common, while those adapted to cooler climatic conditions may decline. Ocean and coastal acidification due to increased atmospheric carbon dioxide could negatively affect shell-building creatures and many other types of estuarine life. The dynamic nature of the Peconic Estuary’s natural resources will require protection of critical habitats both where they exist today and where they may exist in the future.

Completed in 2019, the Peconic Estuary Partnership Climate Vulnerability Assessment and Action Plan, as well as other scientific resources, informed the CCMP 2020 development process and detailed the below information on climate change impacts.

Climate Change Impacts in the Peconic Estuary


Conservative projections for the Long Island region include air temperature increases ranging from 3°F to 6.6°F by 2050, along with greater temperature variability, increased seasonality, and higher frequency of extreme temperature events. Ocean temperatures in our region are expected to rise between 4°F and 8°F over the next century.


While increases in annual precipitation are expected to be relatively minor, the amount of precipitation falling as part of an "extreme" precipitation event and the frequency of such events is expected to increase, an increase in total rainfall of 1% to13% by 2050—periods of drought are also expected to increase.

Sea Level Rise

Globally sea levels are rising in part due to expansion of oceanic waters as average temperatures increase and in part due to increased amounts of available freshwater from melting glaciers and land-based ice. Locally, sea level is expected to increase up to 8 inches by the 2020s, and up to 30 inches by the 2050s. Rising seas are likely to causes stresses on habitat, human populations and natural resources. As sea level increases, we may expect an increase in demand for hardened shorelines. An environmentally beneficial alternative to hardening shorelines is construction of living shorelines which may also have positive impacts on habitat.

Ocean Acidification

As an increasing amount of carbon dioxide (CO2) accumulates in the atmosphere, there is a similar increase in the amount of CO2 that is transmitted to the oceans. When CO2 dissolves in salt water a series of chemical reactions take place that result in a decrease in the overall pH of the water, meaning that the water becomes more acidic. The process is called ocean acidification. The ocean pH is now lower than any time in the last 420,000 years and if current trends continue, the average pH of the oceans could drop by as much as 0.5 pH units relative to preindustrial levels.

Water Quality and Watershed

The Peconic Estuary’s surface waters support valuable habitat, recreation, and fisheries. Groundwater is the primary source of drinking water for the surrounding communities and freshwater for the watershed’s river, ponds, wetlands, and the Estuary itself. It also maintains the estuary’s saline balance.

The watershed’s surface water and groundwater, which are monitored and protected closely, face numerous pressures. Nutrients in groundwater (primarily from septic systems); contaminated runoff from impervious surfaces, lawns, agricultural areas, and golf courses; and atmospheric deposition of nitrogen have affected the Peconic Estuary’s water quality. Changes in precipitation patterns, in particular the projected increases in total precipitation and extreme rain events, will likely lead to increased land based runoff of nutrients, herbicides, and pesticides and may also lead to increased atmospheric deposition. Additionally increases in sea level will likely result in regular inundation of septic systems in coastal communities, either through regular tide cycles or elevation of groundwater level. This will lead to increases in the amount of nitrogen and pathogens transmitted directly to estuarine waters.

Nitrogen pollution is one of the most serious threats to the water quality of the Peconic Estuary, the main cause of hypoxia and HABs, and a contributing factor in the loss of critical eelgrass and wetland habitats.

Groundwater pumping has caused saltwater intrusion and reduced discharges to streams, ponds, coastal wetlands, and estuaries. Climate change has the potential to exacerbate these issues in the following ways:

  • Changes in precipitation—especially the projected increases in total precipitation and extreme rain storms—will likely lead to increased land-based and atmospheric inputs of nutrients.
  • Increased nutrient inputs plus warmer water may lead to more HABs, eutrophication, and hypoxia in salt and fresh surface water. The many impacts of climate change are likely to directly influence the occurrences, types, abundance, distribution and duration of harmful algal blooms in Peconic Estuary waters. Increased nutrient loading to the waters of the Peconic Estuary will provide more food for harmful algal blooms. Additionally, since harmful algal booms generally occur during the warm summer season, increasing water temperatures may result in earlier and more frequent blooms. Warming temperatures could also prevent mixing of the water, and allow the algae to grow thicker and faster.
  • SLR will likely result in the regular inundation of septic systems in coastal communities—either through higher tides or elevated groundwater levels—which could increase the amount of nitrogen and pathogens transmitted directly to estuarine waters.
  • SLR has the potential to change the depth of the interface between freshwater and saltwater, which would threaten Long Island’s drinking water supply and the Peconic Estuary’s freshwater-fed habitats.
Marine Habitats

Climate change is linked to the loss of eelgrass, wetlands, and other marine habitats, which provide an important feeding and nursery habitat for recreational and commercial fisheries.


Wetlands can migrate inshore gradually with rising water levels. However, the rate at which the sea-level is rising is making it difficult for wetlands to migrate inshore fast enough. In many cases around the Peconic Estuary low marsh plants are not able to hold their ground and high marsh plants are becoming more dominant in wetlands. In areas with significant coastal development and shoreline hardening, coastal habitats will be prevented from migrating landwards as sea level rises.

Large areas of wetlands have been protected by municipalities and preservation stewards because they are important to commercial and recreational fishing and as nurseries for aquatic species. Because of their ability to absorb storm energy, wetlands are increasingly seen as a first line of defense against storm surge, adding to their value in land preservation.
Although wetlands can migrate inshore with rising waters , several factors can affect their migration, including the rate of SLR, shoreline type, sedimentation rates, and property development.

Narrow coastal areas can block migration pathways in nearshore
areas. Without sufficient sediment supply, SLR may drown low marsh wetlands if migration pathways are blocked and wetlands are prevented from migrating landward as sea level rises.


Research suggests that rising water temperatures and reduced water clarity are contributing to the loss of eelgrass beds.

Eelgrass is often used as an indicator of estuarine health and water quality. Commonly found in shallow areas of high light penetration, eelgrass is already affected by water quality issues, harmful algal blooms, and boating. Eelgrass may be critically stressed by SLR-induced changes in salinity, water temperature, and ultraviolet radiation if protection measures are
not implemented.

Species Diversity and Populations

The great variety of habitats in the watershed supports diverse plant and animal species and populations. Rising average water temperature can alter the mix of species throughout the Peconic Estuary, Since the estuary consists of a diverse community of native marine species which rely on specific food resources and habitats to survive, it is unclear exactly how a range shift of immigrating warm water tolerant fish species to the estuary and emigrating cold water fish species from the estuary will alter ecosystem dynamics for native community members. Additionally, changing precipitation rates, as well as saltwater intrusion, have the potential to threaten species in the following ways:

  • Warmer temperatures may result in an increase in non-native pests. SLR will increase saltwater intrusion, posing a threat to freshwater plants if saltwater extends landward beyond the current saltwater/freshwater interface, and changing precipitation patterns will affect plant growth.
  • Ocean acidification will hinder the ability of calcifying organisms, such as shellfish, to build their shells or skeletons.
  • Climate change will affect the occurrence, types, abundance, distribution, and duration of HABs in the Peconic Estuary.
CRRA Sea Level Rise Projections for the Long Island Region
The Sea Level Rise (SLR) Protections were taken from the New York State Community Risk and Resiliency Act (CRRA) SLR projections, which were based on the 2014 ClimAID update.



Current Projects

Peconic Estuary Partnership provides program and project updates!

Search here for PEP Program Updates

SCMELC Demonstration Living Shoreline Project

Peconic Estuary Partnership is working with Cornell Cooperative Extension of Suffolk County to complete a demonstration living shoreline project at the Suffolk County Marine Environmental Learning Center (SCMELC) in Southold, NY. The project incorporates smooth cordgrass and ribbed mussels and will be evaluated to determine its ability to provide storm resilience and coastal habitat, but also the shoreline’s effectiveness in reducing nitrogen and pathogen inputs to the Peconic Estuary. The project is expected to be complete in August 2021. See here for the SCMELC Living Shoreline project page.

Peconic Estuary Climate Vulnerability Assessment

In 2016 PEP embarked on a Climate Ready Assessment (CRA) Project with Anchor QEA, LLC. to incorporate climate change into an updated CLPS, to conduct a risk-based climate change vulnerability assessment, and to develop an adaptation action plan consistent with USEPA’s Climate Ready Estuaries Program. PEP has completed a risk-based assessment, to account for future sea level rise, storm inundation and erosion potential. Based on the results of this assessment, a Climate Ready Action Plan was developed to address prioritized climate change risks and vulnerabilities in the Peconic Estuary watershed and the Shinnecock Indian Nation. The intent of the Action Plan is to identify methods to integrate climate change consideration into all phases of planning, design, and execution of the Peconic Estuary Partnership. The Climate Ready Action Plan is a guide for the municipalities and resources managers in the Peconic Estuary and the Shinnecock Indian Nation to adapt to the impacts of climate change. Here is the 2019 Peconic Estuary Program Climate Vulnerability Assessment and Action Plan. Here is the 2019 Shinnecock Indian Nation Climate Vulnerability Assessment and Action Plan.

See here for the interactive Climate-based Critical Lands Protection Strategy and Ranking Tool Story Map!

The Peconic Estuary Partnership will be sharing this information with the municipalities within the Peconic Estuary watershed over the course 2020 and 2021.

Click here for the draft results of the Peconic Estuary Program and Shinnecock Indian Nation Climate Vulnerability Assessment Services project presented by Anchor QEA, LLC. and The Nature Conservancy at the June 5th, 2019 Land Use Stakeholder meeting.

Click here for the Peconic Estuary Partnership and Shinnecock Indian Nation Climate Vulnerability Assessment Services: Risk Assessment presented by Lena DeSantis of Anchor QEA, LLC. at the January 7th, 2019 CCMP Climate Change and Resiliency Chapter Workshop.

Click here for the Climate Ready Assessment of the Peconic Estuary and Shinnecock Indian Nation, and an update to the Peconic Estuary Critical Land Protection Strategy presented by Lena DeSantis of Anchor QEA, LLC. presented at the February 13th, 2018 Technical Advisory Committee meeting.

Considering Climate Change in the Critical Lands Protection Strategy

In 2016 PEP embarked on a Climate Ready Assessment (CRA) Project with Anchor QEA, LLC. to incorporate climate change into an updated CLPS, to conduct a risk-based climate change vulnerability assessment, and to develop an adaptation action plan consistent with USEPA’s Climate Ready Estuaries Program. The PEP completed an update to the Peconic Critical Lands Protection Strategy (CLPS), originally completed in 2004, to take into account climate related variables, specifically sea level rise, in order to update land acquisition priorities. This project will result in the protection and acquisition of lands the will continue to preserve and improve water and habitat quality in the face of rising sea levels and increased temperatures. It will allow for the natural inland migration of critical wetland habitats as sea level rises and preserve living shorelines in an environment where shoreline hardening is likely to become increasingly common. The information resulting from the new strategy will serve as an important tool for New York State, Suffolk County, and local agencies. The 2019 Critical Lands Protection Strategy is included here in the 2019 Peconic Estuary Partnership Climate Vulnerability Assessment and Action Plan.

See here for the interactive Climate-based Critical Lands Protection Strategy and Ranking Tool Story Map!

The Peconic Estuary Partnership will be sharing this information with the municipalities within the Peconic Estuary watershed over the course 2020 and 2021.

Erosion behind a bulkhead on the shore.

PEP’s Critical Lands Protection Strategy Criteria and Ranking Tool

In the face of climate change impacts – specifically sea level rise – we need to be strategic in adapting. PEP developed the Critical Lands Protection Strategy (CLPS) in order to inform land acquisition priorities and reach land protection goals.

Did you know that protecting land can increase resiliency and improve water quality?
Protecting land not only provides safe haven for wildlife species, but it also provides:

  • Wetland habitats the room to migrate inland as sea level rises
  • ‘Living shoreline’ project opportunities that strengthen our shores from storm surges while also preserving open access to our bays
  • Protection of our groundwater from unwanted pollution and the ability to better handle flooding as water tables rise

If we can prioritize the parcels of land that will provide the greatest potential to protecting and preserving the health of the estuary, then we can move forward in making informed decisions about our land – building a cleaner and more resilient future.

To make this easy, we have developed The Critical Lands Protection Strategy Criteria and Ranking Tool!

This tool assigns a priority score to individual parcels of land based on how they meet or do not meet our carefully selected criteria. We ask questions like – Is this parcel of land located in an area that will become inundated under future sea-level rise projections? Does this parcel of land contain or will contain freshwater or tidal wetlands?  We have organized criteria like these into three groupings with the goals of:

This information has been transformed into interactive maps! Municipalities, land stewards, and decision makers alike can use this tool to help decide which lands to acquire and evaluate which climate adaptation strategy is appropriate. This tool will help us make land management decisions that will matter for habitat and water quality protection, now and in the future.

PEP hosted a virtual workshop to guide you in using our interactive story map and ranking tool.

Explore the story map that will allow you to identify land priorities and equip you with next actions to take.

This tool is a component of the PEP 2020 Comprehensive Conservation and Management Plan. Click here to read our plan that contains Goals and Actions we will work towards over the next decade, bringing us closer to achieving our mission of protecting and restoring the Peconic Estuary and its watershed.

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