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Ken Zegel

PE, Principal Public Health Engineer


 360 Yaphank Avenue
Suite 2B
Yaphank, New York 11980

(631) 852-5750

Fax: (631) 852-5812

Office of Ecology

The Office of Ecology (OE) has responsibility for monitoring and protecting the environment and ecological resources of the County, including groundwater, marine and fresh waters, wetlands, other natural resources, and permitting and inspecting bathing beaches. Under the auspices of the National Estuary Program (NEP), a federal program established to study, protect and preserve nationally significant estuaries threatened by pollution, development or misuse, OE serves as the project office for the Peconic Estuary Program (PEP). The OE also participates in the Long Island Sound Study (LISS) and the South Shore Estuary Reserve (SSER), and provides program management for the Comprehensive Water Resources Management Plan, serves on the department’s Board of Review, participates on the County’s numerous advisory committees dealing with environmental issues and provides certification of ecological and marine productivity criteria for County dredging projects.

The Office of Ecology contains two major bureaus: Environmental Management and Marine Resources. The Bureau of Environmental Management is responsible for the administrative and technical aspects of the PEP, coordination of the LISS and SSER, the SEQRA reviews of the division, and technical support for the county’s Pesticide Reduction Plan and Wetlands Stewardship initiative. The Bureau of Marine Resources is responsible for the bathing beach sampling, inspection, and permit program, water quality monitoring in the Peconic Estuary, the Long Island Sound and adjacent embayments, the South Shore Estuary (including the Forge River and Beaver Dam Creek studies), and for the monitoring and investigation of Harmful Algal Blooms, including Brown Tide, Red Tides, the Rust Tide and Cyanobacteria.


Bureau of Environmental Management

The Bureau of Environmental Management’s primary goals are protecting the environmental and ecological resources of the county including groundwater, marine and fresh waters, natural habitats, other natural resources through participation in programs that develop, oversee or review environmental studies, implementation programs, land use plans, and impact statements to safeguard the quality of Suffolk’s groundwater and surface water resources, by preventing or mitigating activities that may degrade the environment, and to conduct outreach programs to educate the public.
The Bureau is responsible for the administration and technical aspects of the Peconic Estuary Program, coordination with the Long Island Sound Study and South Shore Estuary Reserve activities, county reviews under the State Environmental Quality Review Act (SEQRA), participation in the county’s Aquaculture Lease Program and Water Quality Protection and Restoration Program (Suffolk County’s 1/4% Sales Tax Program), and participation with various advisory committees dealing with environmental issues.

Peconic Estuary Program (PEP)

The Peconic Estuary is one of 28 estuaries in the National Estuary Program (NEP), administered by the United States Environmental Protection Agency (USEPA) under the auspices of Sec. 320 of the Clean Water Act to protect and preserve nationally significant estuaries which are threatened by pollution, development, or overuse. The Peconic Estuary was accepted into the program as an “estuary of national significance” in 1992.
The SCDHS, Office of Ecology operates the PEP Program Office and provides the day-to-day management functions and the technical and administrative support to the program, and conducts a comprehensive water quality monitoring program throughout the estuary. Three additional committees within the Program, the Technical Advisory Committee, the Citizens Advisory Committee, and the Local Government Committee, are comprised of technical experts and federal, state, and local officials, as well as citizens. These stakeholders, collectively known as the PEP Management Conference, completed the final Comprehensive Conservation and Management Plan (CCMP), designed to protect and preserve the Peconic Estuary, in November of 2001. For more information on the Peconic Estuary Program, visit the programs website ( or click on the link below.

Marine Water Quality Monitoring Program

The office conducts environmental and water quality monitoring along 990 miles of the county’s marine coastline in support of the Peconic Estuary Program, Long Island Sound Study, South Shore Estuary Reserve, and the NTN/National Atmospheric Deposition Program. Parameters analyzed include total and fecal coliform bacteria, nitrate+nitrite-nitrogen, ammonia-nitrogen, total and dissolved nitrogen, total and dissolved phosphorus, total suspended solids, and chlorophyll-a. Salinity, temperature, dissolved oxygen, and secchi depth measurements are also taken. Harmful algal bloom (HAB) monitoring is performed for brown tide (Aureococcus anophagefferens), Cochlodinium polykrikoides (a form of red tide), and Cyanobacteria (a potentially toxic blue-green algae). These monitoring efforts and the extensive data gathered are the centerpiece of many technical investigations and studies performed by both government and university researchers concerning the health of our bays.

State Environmental Quality Review Act (SEQRA)

The Office conducts administrative and management activities, and provides expanded technical commentary as required by SEQRA and County mandate. Detailed technical comments are provided for major private and municipal development proposals, as well as for state and municipal planning studies (master plans, open space, Pine Barrens, etc.).

Special Monitoring

In response to requests from elected officials, agencies and complaints from citizens, events occurring in the marine environment are investigated and samples collected as required. Phenomena typically investigated include discolored waters, plankton blooms, fish kills, unusual odors, wash-ups of floatables, marina pump-outs, shellfish sanitation, wastewater discharges, and aquatic dermatitis. Two ongoing projects involve investigations into water quality impairments in two south shore tributaries, the Forge River in Mastic and Beaverdam Creek in Brookhaven.

Bureau of Marine Resources

The Bureau of Marine Resources is responsible for the bathing beach sampling, inspection and permit program; water quality monitoring for the Peconic Estuary Program, South Shore Estuary Reserve and the Long Island Sound Study; monitoring and investigation of Harmful Algal Blooms, including the Brown Tide; and numerous special projects and investigations regarding surface waters in the county.

National Trends Network

With support from the Peconic Estuary Program (PEP), and as a participant in the National Atmospheric Deposition Program’s (NADP) National Trends Network (NTN), the Office has operated a solar-powered rainfall/deposition monitoring station at Cedar Beach in Southold since 2003. The station gathers data on the concentration of contaminants including acid rain and nitrate-nitrogen, and provides valuable information regarding local environment impacts from atmospheric deposition.
In 2013, through a partnership between the PEP and the New York State Environmental Research and Development Agency (NYSERDA), mercury deposition was added as a monitoring parameter.

Long Island Sound Study (LISS)

The LISS is also funded under the auspices of the NEP and is currently implementing its CCMP. Among the goals is improvement of oxygen levels in the sound through reduction of nitrogen input. As part of that effort, the Office was selected by the NYSDEC to conduct a study, the North Shore Embayment Watershed Management Plan. The report shows that groundwater is the largest contributor of nitrogen to the sound from our Management Zone. Nitrogen from groundwater in terms of magnitude is followed by atmospheric deposition, stream flow, sewage treatment plant discharges and stormwater. The relative nitrogen inputs create a significant challenge to achieving the goal of a 58.5% reduction in nitrogen.

YSI Automated Water Quality Monitors

The Office deploys several YSI automated water quality monitors (sondes) that are configured to measure temperature, salinity, dissolved oxygen, and chlorophyll-a, at 15-minute intervals. The data collected has been utilized in the development of a nitrogen/dissolved oxygen TMDL for the western Peconic Estuary, has provided valuable information on conditions in areas that were once hot-spots for "brown tide" (Flanders Bay and West Neck Bay), and has contributed to the Suffolk County Northshore Embayments Watershed Management Plan as well as the Forge River Watershed Management Plan.

Bathing Beach Program

The Office regulates all bathing beaches in the county under §6-2 of the NYS Sanitary Code to ensure compliance with water quality, safety and supervision standards. Each permitted beach facility is inspected annually with follow-up visits made as necessary. The federal Beaches Environmental Assessment & Coastal Health (BEACH) Act Grant provides $100,000 annually to directly support county staff and sampling supplies. Water quality monitoring to determine the presence of potentially pathogenic organisms is conducted at approximately 200 beaches each season. Using a risk-based approach, more frequent sampling is concentrated at those beaches with known poor water quality. In general, these include beaches that are proximate to pollution sources or are poorly flushed. As required by the BEACH Act, and incorporated into the NYS Sanitary Code in June 2004, Enterococci and E.coli bacteria are utilized as indicator organisms for assessment of beach water quality. The frequency and extent of water quality monitoring has dramatically increased in recent years, reflecting implementation of the BEACH Act and the county’s commitment to public health by providing safe and clean recreational beaches. The expanded monitoring effort has also resulted in an increased number of bathing advisories and beach closures.

Vector Control & Wetlands Management Plan

The Suffolk County Department of Health Services and Suffolk County Department of Public Works oversaw the development and early implementation of a Suffolk County-wide long-term vector control and wetlands management plan. The overall goals were to: protect public health while minimizing pesticide usage; and to develop a long-term plan to preserve and restore wetlands managed by Vector Control. The management plan and accompanying generic environmental impact statement (GEIS) have been developed by a consultant team, with support from other entities, including the County, at a contracted cost of approximately $4 million. Highlights include the elimination of routine ditch maintenance, a larvicide reduction goal of 75% and reductions in chemical adulticide usage, and restoration of 4,000 acres of ditched wetlands over the next 12 years. The risk assessment specifically evaluated human health and ecological risks associated with the pesticides considered for use and concluded that Ultra Low Volume (ULV) insecticide applications for mosquito control do not pose a significant threat to human health. In addition, no risks were found for mammalian, avian or reptilian wildlife. Potential ecological risks were limited to non-target terrestrial insects from adulticides which can be mitigated or eliminated by Integrated Pest Management (IPM) strategies and possible short term impacts to some aquatic invertebrates if it becomes necessary to apply Malathion. The success of Open Marsh Water Management (OMWM) practices was demonstrated at a 40-acre wetland on the Wertheim National Wildlife Refuge. The parcel was routinely subjected to larvicide applications, but none were needed in 2005 following OMWM implementation.

Suffolk County Government

H. Lee Dennison Bldg

100 Veterans Memorial Hwy
P.O. Box 6100
Hauppauge, NY 11788

Riverhead County Center

County Road 51
Riverhead, NY 11901