Suffolk County Continuous Monitoring Stations

Suffolk County of Marine Resources has routinely monitored the water quality of surface and marine waters in the Peconic Estuary on a monthly basis since 1977 throughout 38 marine locations as well as an additional 2 stream and point source sites. This data is sufficient to document seasonal variability and trends in the waterbodies being measured.

More information about the monitoring program as well as publicly available data can be found on the Suffolk County Marine Water Quality Monitoring website. SCDHS also conducts a comprehensive bathing beach water quality monitoring program from May through September. A telephone Beach Hotline message (631-852-5822) is regularly updated to reflect any changes in beach status. 

WaterTraq, the Long Island Water Quality groundwater viewer hosted by the Long Island Commission for Aquifer Protection, allows water suppliers, health officials, industry professionals, and the public to research contamination by location. Explore these interactive maps to learn more about water quality across Long Island!

Sampling analysis at marine stations includes:

• Total and dissolved nitrogen 
• Total and dissolved phosphorus
• Carbon (TOC, DOC mg/L)
• Dissolved inorganic nitrogen (nitrate, nitrite, ammonia)
• Dissolve ortho-phosphate
• Total and fecal coliform bacteria
• Total suspended solids
• Chlorophyll-a
• Brown tide algal species

Physical measurements taken include: 

• Salinity
• Temperature
• Dissolved oxygen
•  pH
• Light attenuation (PAR)
• Secchi depth

Freshwater sample are also analyzed for dissolved metals and organic compounds, including radiologicals, chloride, sulfate, pesticides and herbicide compounds.

USGS Continuous Water Quality Monitoring

The Peconic Estuary Partnership partnered with Suffolk County and the United States Geological Survey (USGS) to install three continuous water quality monitoring stations within the Peconic Estuary:

• Orient Point Harbor
• South side of Shelter Island
• At the mouth of the Peconic River under the 105 bridge in Riverhead.

Together, these three monitoring systems provide temporal and spatial sampling of water quality in the estuary with data collection occurring every 6 minutes. For more information, see the USGS data for each station, at the Peconic River, Shelter Island, and Orient Point Harbor.

At 6 minute intervals, the following is measured: 

• Ocean and estuary elevation
• Water temperature
• Specific conductivity
• Salinity
• Dissolved oxygen
• Turbidity
• Chlorophyll
• Sampling depth
• pH

Nitrate is measured every 30 minutes in the water column. 

Suffolk County Continuous Water Quality Monitoring Stations

From May through October the NYS Department of Environmental Conservation compiles and provides notifications of known HAB locations in New York State water bodies. NYSDEC also provides information on consistent and temporary shellfish closures. For more information check out the NYSDEC Public Shellfish Mapper – an interactive map showing shellfish closures, conditional harvesting programs, shellfish harvest zones, aquaculture lease sites, and water sampling locations. For the most up to date temporary emergency closure information please call the hotline at (631) 444-0480. A recorded message is available 24 hours a day including weekends. For any other questions call the main shellfish office at (631) 444-0492 during normal business hours, M-F 8:30 AM until 4:45 PM.

As of 2025, PEP has launched its seagrass monitoring program in partnership with researchers from Stony Brook University. 

This monitoring program continues to focus on collecting data pertaining to the health of eelgrass beds at various sites throughout the Peconic Estuary. PEP continues to support aerial surveys of eelgrass and continues monitoring the successful work that has come from the Coastal Watershed Grant.  PEP hopes that this continued work will assist New York State’s initiatives to create seagrass management areas in the near future. 

Eelgrass monitoring program measures: 

• Water temperature
• Sediment samples (lab analysis for percent organic content)
• Fauna counts
• Light measurement
• Salinity
• Macroalgal percent cover and identification
• Eelgrass bed aerial extent
• Eelgrass shoot density
• Temperature
• Light loggers are deployed for extended periods of continuous sampling during the growing season.

Cornell Cooperative Extension of Suffolk County, Stony Brook University, and PEP work annually with New York State Department of Environmental Conservation to coordinate and implement the NY Horseshoe Crab Monitoring Network. 

Horseshoe crabs have been estimated to be almost 450 million years old; yet, have evolved and changed very little during that time. Horseshoe crabs play an important role in the marine food web, producing eggs that are an essential energy source for migrating shorebirds such as the Red knot. Research on horseshoe crab anatomy and physiology has allowed scientists to learn more about a variety of topics impacting everything from human health to space travel. Horseshoe crabs even play a vital role in the biomedical industry. The bright-blue blood of the horseshoe crab contains a protein called Limulus Amebocyte Lysate (LAL), which is used by pharmaceutical and medical device manufacturers to test their products for the presence of endotoxins and bacterial substances that can cause fevers and even be fatal to humans. The horseshoe crab survey is one of PEP’s many citizen science activities that engages the public in habitat restoration and wildlife projects, thereby increasing the public’s understanding of the importance of Peconic Estuary Watershed as well as bolsters support for habitat and wildlife restoration and protection efforts. Every year PEP trains volunteers who participate in monitoring Horseshoe Crab populations in the Peconic Estuary Watershed. The annual horseshoe crab monitoring survey is essential to assessing the status of horseshoe crabs in New York’s Marine District, and to assist with the regional management and conservation of this important species through the Atlantic States Marine Fisheries Commission.

Horseshoe Crab Monitoring Sites in the Peconic Estuary Watershed:

Map of New York State Horseshoe Crab Monitoring Network Sites in the Peconic Estuary Watershed.

• South Harbor Park, Southold (2013 to present)
• West Creek, Southold (2017 to present)
• Squires Pond, Hampton Bays (2011 to present)
• Northwest Harbor, East Hampton (2019 to present)
• Napeague Bay, East Hampton (2019 to present)

What is sampled?

The Horseshoe Crab Monitoring program measures: spawning abundance, size, sex, shell condition, number of tagged, and tag returns around full and new moon events in May, June, and July. Additionally, environmental parameters, air and water temperature, wind speed, sea state, cloud cover, and tide cycle are recorded every survey night.

To volunteer for the Horseshoe Crab Monitoring program, email Valerie Virgona at valerie.virgona@stonybrook.edu.

Over the last several decades, PEP has been diligently working with its partners to restore historic critical freshwater spawning and maturation habitat for diadromous fish in the Peconic Estuary Watershed.

Through the installation of fish passage structures and replacing undersized road culverts with larger, fish friendly culverts, PEP and our partners have provided several ways for alewives and American eels to go around or over the dams to reach critical spawning habitat. The two largest alewife spawning runs on Long Island occur in the Peconic Estuary Watershed.

Alewife monitoring at Grangebel Park, the mouth of the Peconic River, has been carried out annually since 2018 by volunteer partners at Suffolk County Community College. Grangebel Dam was the first barrier on the main stem of the Peconic River and the first one to have a fish passage built on it. Construction of the Grangebel Nature-like Fishway, opened up 1.5 miles of river as well as 25 acres of diadromous spawning and maturation habitat at the start of the Peconic River. Thousands of alewives use the fishway each year. Supplementally, annual video monitoring of diadromous fish at Grangebel Nature-like Fishway and additional PIT tagging occurs to collect data on the river herring and analyze the populations using these fish passages. This data will be provided to the New York Department of Environmental Conservation and the Atlantic States Marine Fisheries Commission to aid in stock assessments and the management of alewife.

What is sampled?

PEP’S annual alewife monitoring at Grangebel is conducted in three ways:

1. Visual counts are conducted by trained volunteers/interns, wherein they inspect or watch a site for fixed durations of time, and then make an estimate of how many fish are present.
2. Video counts are obtained from recorded video footage that is retrieved or downloaded at least twice per week. This footage is analyzed by trained PEP interns who identify and count the alewife.
3. Biological monitoring data is collected from adult alewives caught by cast nets, dip nets, or hand harvesting. Alewives are measured, sex is determined, and then, scales are retrieved for age determination. Afterwards, the alewives are released. A subset of fish (up to 300/year) are given Passive Integrated Transponder (PIT) tags just under their skin. PIT tags give alewife an unique identifier; thereby, allowing its migration to be logged when the alewife travels near receiver PIT tag antennas throughout the Peconic Estuary Watershed. The PIT tag provides a correction factor for the double counting that is associated with some alewives that circle back between the lower reaches of the Peconic River and upstream spawning ground habitat.

Until recently, the Peconic River had six dams along its length that prevented diadromous fish species from migrating up and downstream.

Currently, four out of the six dams have had fish passages built, restoring over three hundred acres of diadromous fish habitat on the Peconic River. The installation of fish passages supports the access to freshwater spawning habitat for diadromous fish populations in the Peconic River and tributaries. Revitalizing and strengthening ecosystem services, fish, and wildlife of the Peconic Estuary will benefit from access to critical habitat, increased biodiversity, and restoration of historic food webs. PEP and partners can accurately track alewife abundance in the Peconic River, evaluate the success of fish passage restoration efforts, and guide management of the species.

The Long Island Volunteer River Herring and Eel Survey is led by Seatuck Environmental Association, having started in 2006 alongside several partners, including PEP, Long Island Sound Study, and South Shore Estuary Reserve. It is the longest running community science project on Long Island. PEP leads this citizen science initiative throughout the Peconic Estuary Watershed to identify potential additional alewife habitat. This monitoring is critical and important to PEP and their partners as the observations validate which runs are viable and most likely to benefit from financial investment on fish passages for spawning habitat restoration. During the annual survey, volunteers are trained by PEP through River Herring and Eel Survey Guidelines, to survey local waterways in the Peconic Estuary Watershed from mid-March through mid-May. This survey engages community scientist volunteers to monitor historical runs of migratory river herring and American eels in rivers and streams across Long Island. Additionally, this helps the public to become educated on alewife and get motivated to become involved in monitoring and river connectivity issues in the Peconic Estuary.

What is sampled?

On each river herring site visit, citizen scientists records the date, time, tributary/observation site name, GPS coordinates, tidal stage, and water temperature.  They then look for river herring and American eel presence, other species presence, estimation of the size of the spawning run, take site photos, and record supplemental interesting observations. The information from the survey can also submitted through an easy-to-use on-line application, Survey123 field app, via computer or mobile device and automatically becomes part of the Long Island Volunteer River Herring and Eel Survey Database.

To volunteer for the river herring and eel surveys, email Valerie Virgona at valerie.virgona@stonybrook.edu.

Marine and estuarine systems face a myriad of stressors ranging from eutrophication, habitat alteration, overfishing to ocean warming.

Since 1987, the New York State Department of Environmental Conservation has conducted an extensive trawl survey in the Peconic Estuary, partnering alongside Stony Brook University and PEP. Trawl survey partners analyze the spatial and temporal trends in the Peconic Estuary finfish trawl survey dataset and develop risk metrics from ecological relationships for the Peconic Estuary that examine whether local and regional environmental changes have increased the vulnerability of individual finfish and mobile invertebrate species, community assemblages, and ecosystem processes. This survey is carried out May through October with a 4.9-meter semi-balloon otter trawl. Sixteen stations are chosen weekly from a block grid of 77 units, each 1’ latitude by 1’ longitude in size. On average, 381 tows are collected each year. 

Assessing the vulnerability of species and communities to environmental change in the Peconic Estuary has direct application to decisions affecting the use, management, and conservation of the natural resources in the bay. Trawl survey data helps to satisfy the compliance requirements of interstate fishery management plans for New York. It informs a number of stock assessments for important finfish and crustacean species. It is used in the development of dredging windows to protect vulnerable species such as winter flounder. Stony Brook University uses the trawl data for Graduate and PhD research programs and projects. New York State Department of Environmental Conservation and Suffolk County also incorporate this information into their decision-making evaluating proposed locations for shellfish aquaculture in the Aquaculture Lease Program.

What is sampled?

Map of Peconic Estuary survey blocks used in the NYSDEC

The trawls begin near the center of each randomly selected block as seen in the Map of Peconic Estuary Trawl Survey. Peconic Estuary Trawl Survey utilizes a 4.8 semi-balloon shrimp trawl with 3.8cm mesh in the body, 3.2cm mesh in the code, and 1.3cm mesh in the liner. Fish and mobile invertebrates in the tows are identified, measured and counted, with environmental data (surface and bottom temperature, salinity, dissolved oxygen, tow start depth, GPS location and depth are recorded at the beginning and end of each tow, secchi disc depth) also being recorded. Adult horseshoe crabs and blue crabs are tagged before release. Chlorophyll measurements are obtained from the Suffolk County Department of Health Services. Two climatic indices are also used in the Peconic Estuary Trawl Survey analysis, the Atlantic Multi-Decadal Oscillation Index (AMO) and the North Atlantic Oscillation Index (NAO) obtained from the National Oceanic and Atmospheric Administration.

The Surface Elevation Table (SET) is a portable mechanical leveling device for measuring the relative elevation change of wetland sediments. 

SET monitoring measures the degree of accretion or subsidence on the marsh surface through relative elevation data.

Peconic Estuary Partnership measures the surface elevation of the salt marsh at Indian Island County Park, Hubbard County Park, and Cedar Beach of Southold Town. There are multiple elevation tables at each site that measure marsh accretion or subsidence, natural processes that are influenced by sea-level rise, changes in sediment loading, increasing temperatures, and other consequences of climate change. Monitoring is conducted annually, with data contributing to local and regional understanding of the status and future of salt marsh systems in a changing environment.