Peconic Estuary Water Quality Report

Higher water clarity means that more sunlight can reach submerged aquatic vegetation (SAV), such as eelgrass, which needs sunlight to grow and survive. 

SAV provides important habitat for marine life, but reduced water clarity can limit how much light reaches the bottom of the estuary where SAV grows. Increased algal blooms in the water column can also lead to lower light availability for SAV like eelgrass. Chlorophyll-a is the photosynthetic pigment in plants and algae that absorbs sunlight and facilitates photosynthesis. Therefore, chlorophyll-a concentrations in the water can be an indicator of the amount of algae in the water.

Water clarity in the PEP Annual Water Quality Report is measured by a Secchi disk depth, which is a white and black disk lowered in the water. The depth at which the disk is no longer visible is used as a measure of how clear the water is. Higher water quality is indicated by a greater Secchi disk depth.

Nitrogen is an essential nutrient for healthy ecosystems.

However, too much nitrogen, including nitrogen pollution from human sources, can lead to excessive algal growth and subsequent poor water quality. In the Peconic Estuary, nitrogen pollution is one of the greatest threats to water quality. The western part of the estuary is particularly susceptible to increasing nitrogen loading due to the presence of multiple pollution sources and low tidal flushing. The PEP Annual Water Quality Report measures total nitrogen across the Peconic Estuary to help inform the health of our waters.

Dissolved oxygen in the water column is necessary for fish and other aquatic life to live.

Low levels of dissolved oxygen (DO), also called hypoxia, can be caused by too much algae in the water, as well as natural variations in temperature, wave action, and mixing. Algae produce oxygen during the day through photosynthesis, but at night they consume oxygen through a process called ‘respiration’. If there is too much algae in the water consuming lots of oxygen, hypoxia can occur during the night and early morning. Oxygen is also consumed by bacteria as they eat algae that have died and sunk to the bottom.

Hypoxia can have far-reaching effects across an ecosystem. The PEP Annual Water Quality Report includes measurements of DO by two U.S. Geological Survey continuous monitoring stations, one in the Peconic River and one in Orient Harbor. These measurements are taken every 6 minutes and can be used to look at the average DO concentrations, as well as the number of days each month where DO falls below PEP target thresholds.

Increased nitrogen loading has been linked to the presence of Harmful Algal Blooms (HABs) in the Peconic Estuary.

Blooms have been observed in the Estuary since in June of 1985, when an unusually large and persistent bloom of the algae called “brown tide” was first observed. Brown tides continued to occur at high concentrations and for extended periods throughout the Estuary through the 1990s, leading to declines in eelgrass and bay scallop populations. These occurrences were the main catalysts for the creation of the Peconic Estuary Partnership.

While brown tides are less common now, other harmful algal blooms have been increasingly documented across the estuary in recent years. Some HABs can produce toxins that directly impact humans or fish and shellfish. However, HABs can also have secondary effects. As algal cells die and sink to the bottom they are consumed by bacteria, which also use oxygen as they consume the algae, leading to hypoxia.

Presence of algal species around Long Island, updated as of Summer 2025. Please note that the boundaries in this map are approximate, it should not be assumed that each occurrence covers 100% of the areas that are delineated.

Other blooms commonly observed in the Peconic Estuary include:

• “Red Tides”, caused by the dinoflagellate Alexandrium catenella. This algae produces a neurotoxin called saxitoxin, which can cause Paralytic Shellfish Poisoning (PSP), a potentially fatal illness. Humans can be exposed to PSP by eating bivalves like oysters, clams, or mussels contaminated by saxitoxin produced by Alexandrium blooms.
• Dinoflagellate Dinophysis acuminata, which produces a toxin called okadaic acid and can cause Diarrhetic Shellfish Poisoning (DSP), an acute gastrointestinal illness. Humans can get DSP by consuming bivalves contaminated with okadaic acid from Dinophysis blooms.
• Toxic blue-green algae blooms caused by Cyanobacteria sp. have also been observed in both marine and freshwater.

There are also non-toxic blooms that are periodically present in the Peconic Estuary, inculding:

• “Rust Tides” caused by Margalefinidium (formerly Cochlodinium) polykrikoides 
• Mahogany Tides commonly caused by Prorocentrum minimum.

Suffolk County conducts seasonal HAB monitoring in conjunction with several partners, including the New York State Department of Environmental Conservation and the Gobler Lab at Stony Brook University. PEP has committed to tracking and reporting on HABs on an annual basis. 

Pathogens are viruses, bacteria, fungi, and protozoans that cause diseases in humans, other animals, or plants.

The potential for the presence of human pathogens in water is measured using bacterial indicator species such as fecal indicator bacteria. Fecal indicator bacteria (FIB), including total and fecal coliform bacteria, originate in the intestines of warm-blooded animals. Their presence in the water indicates that the waste of an animal, which may contain pathogens, has entered the water. Water quality at swimming beaches can be adversely affected by potential pathogens through episodic sources such as stormwater runoff, wastewater discharges from boats or septic systems, and waste from pets and wildlife. Suffolk County Department of Health Services conducts a comprehensive bathing beach water quality monitoring program in the Peconic Estuary from May through September, monitoring for a type of FIB called Enterococcus. The map below shows the locations of beaches that are monitored for Enterococcus. Suffolk County bathing beaches in the Peconic Estuary watershed and Tier 2 and Tier 3 beaches, meaning they have a low to moderate relative risk associated with their use. Relative exceedances of bacterial concentrations over the target threshold provide a coarse measure of potential risk of exposure to harmful pathogens, and provides a framework for identifying locations that may need management actions to remediate potential public health issues.

Map of Bathing Beaches Across the Peconic Estuary Monitored by SCDHS.

Note: Monitoring of coliform bacteria and classification of shellfish growing areas is conducted by the NYSDEC, Division of Marine Resources Shellfish Sanitation Unit. The NYSDEC Public Shellfish Mapper classifies shellfish growing areas as certified (open) or uncertified (closed) based on the results of their surveys. That information is not present in the PEP report.