Stormwater Management

What is Stormwater?

Stormwater is the portion of precipitation from rain, snowmelt, and other weather events that does not infiltrate into the soil but flows over the land to surface waters. As the stormwater runoff flows over the land or impervious surfaces (such as roads, parking lots, and driveways), it may accumulate debris, chemicals, sediment, or other pollutants that could adversely affect water quality in the receiving waterbody.

Why is polluted stormwater runoff an issue?

Polluted stormwater runoff may impact streams, ponds, wetlands, and other waterways in a variety of ways. For example, transported soil may cloud the waterway and interfere with the habitats of fish and plant life. Nutrients such as phosphorous and nitrogen (found in fertilizers) can promote the overgrowth of algae, deplete oxygen in the waterway, and be harmful to other aquatic life. Toxic compounds from automotive fluids, sediment and construction activities, and careless application of pesticides and herbicides threaten the health of the receiving waterway and can kill fish and other aquatic life. Bacteria from human and animal wastes can make nearby waterbodies unsafe for swimming, fishing, and shellfishing.

What is the government doing about pollution from stormwater runoff?

Under the Clean Water Act, the United States Environmental Protection Agency (EPA) enacted regulations that are intended to protect waterways and waterbodies from pollution and to protect our lands from further harm due to the effects of polluted stormwater. The New York State Department of Environmental Conservation (NYSDEC) is approved by the EPA to administer a program and issue General Stormwater Discharge Permits. These Permits regulate the pollution of the waters of the United States by Municipal Separate Storm Sewer Systems (MS4s).

Where does the Village of Port Jefferson fit in?

The Village of Port Jefferson is designated as an MS4 and is mandated under the requirements of the Permit to meet minimum requirements in six different management practices: Public Education and Outreach; Public Involvement / Participation; Illicit Discharge Detection and Elimination; Construction Site Stormwater Runoff Control; Post-Construction Stormwater Management; and Pollution Prevention / Good Housekeeping for Municipal Operations. The Village is responsible for maintenance of the MS4 as well as ensuring that all development taking place within the Village complies with NYSDEC regulations.

Where can I get information on the Village’s stormwater management program?

Each year, the Village must submit an annual report to update the NYSDEC on the activities of its program to demonstrate that it is following the requirements of the Permit. The most recent annual reports are provided below.

2015-2016 Annual Stormwater Report
2014-2015 Annual Stormwater Report
2013-2014 Annual Stormwater Report
2012-2013 Annual Stormwater Report
2011-2012 Annual Stormwater Report
2010-2011 Annual Stormwater Report
2009-2010 Annual Stormwater Report

Storm Sewershed Map

Each MS4 is required to provide a map of the storm drains and to have a map of the storm sewershed. The maps are provided below.

Storm Drain Map
Storm Sewershed Map

Water Quality Data

Each MS4 is required to provide data on water quality trends related to stormwater. For the purpose of reducing pathogen loading in Port Jefferson Harbor, two parameters (fecal coliform and total coliform) were selected to create water quality trend charts. In general, the downward trends of fecal coliform and total coliform concentrations in the Harbor suggests that progress is being made toward meeting the goals of the Total Maximum Daily Loads (TMDL) for pathogens. The most recent Water Quality Trends report is provided below:

Water Quality Trends for Port Jefferson Harbor


Pathogens are viruses, bacteria, algae, and protozoans that cause diseases in humans, other animals or plants. Pathogens can enter waterways via untreated or partially treated human sewage and possibly by way of wild or domestic animal waste. Humans may encounter pathogens through direct contact with contaminated water, ingestion of contaminated water, or consumption of raw or partially cooked shellfish harvested from contaminated waters. Pathogen inputs to Port Jefferson and Mt. Sinai harbors are a concern because of the potential human health risks and the economic losses associated with the closure of shellfish beds and beaches.

Because measuring concentrations of specific pathogens in salt water is so difficult, fecal and total coliform bacteria is used as an indicator to measure pathogen levels in the water. Excessive levels of coliform bacteria are generally found in areas where tidal flushing is limited and runoff from surrounding land is high.

Stormwater runoff is the largest contributor of pathogens to the local harbors. Sources of pathogens are wildlife (including waterfowl), domestic animals, and poorly functioning septic systems. In addition, another contributor of pathogens is sanitary wastewater from boats. Pathogens can also originate from point source discharges, including effluent from the sewage treatment plant in Port Jefferson Harbor.

What the Village is Doing to Reduce Pathogen Loads

  • Adoption of Pet Waste Ordinance – The Village of Port Jefferson has a local law prohibiting pet waste on municipal properties. This local law was adopted on 5-14-1992 as Local Law No. 3-1992. Additionally, pet waste bags are also provided at select locations in the downtown area of the Village.
  • Adoption of Ordinance Prohibiting Feeding of Waterfowl – The Village of Port Jefferson has a local law prohibiting feeding of waterfowl on publicly owned lands within the Village of Port Jefferson. This local law was adopted on 4-19-2010 as Local Law No. 4-2010.
  • Vessel Waste No Discharge Zone – The entire Port Jefferson Harbor complex has been designated as a Vessel Waste No Discharge Zone (NDZ), making it mandatory to either pump-out your waste to a legal pump-out facility or store it in a certified holding tank on board. The Town of Brookhaven operates a pump-out boat (at no charge) in Port Jefferson and Mt. Sinai Harbors.



Informing residents, businesses, and municipal employees about potential water quality impacts that may be caused by polluted stormwater runoff is key to our stormwater program. Below is a list of publications, geared toward the general public, that outline potential impacts from polluted stormwater runoff and/or steps the community can take to reduce those pollutants.

General Stormwater Publications

Lets Talk About Poop

Lets Talk About Poop
Learn how you can greatly improve water quality in Port Jefferson Harbor and Mt. Sinai Harbor by picking up after your pets, resisting the urge to feed waterfowl, and properly disposing of sanitary waste from your boat.

Boater’s Guide to No-Discharge Zones and Pump-Out Facilities

Boater’s Guide to No-Discharge Zones and Pump-Out Facilities – Boater’s Guide to No-Discharge Zones and Pump-Out Facilities – The Port Jefferson Harbor Complex and Long Island Sound are designated as No Discharge Zones; therefore, overboard discharge of boat sewage into these waters is prohibited. Learn more about No Discharge Zones and boat sewage pump-out facilities available in Port Jefferson Harbor.

A Citizen’s Guide to Curbing Polluted Runoff

A Citizen’s Guide to Curbing Polluted Runoff – This short brochure provides tips on a wide variety of ways to prevent stormwater pollution.

Animal Waste and Water Quality

Animal Waste and Water Quality – Animal waste in stormwater runoff is one source of pathogens in Port Jefferson and Mt. Sinai Harbors. Learn about the affects of animal waste on water quality and ways to keep animal waste from entering our streams and harbors.

Managing Stormwater Runoff in Port Jefferson

Managing Stormwater Runoff in Port Jefferson – This leaflet provides a general overview of the stormwater management efforts in Port Jefferson.

Pathogens Fact Sheet

Pathogens Fact Sheet – Pathogens are viruses, bacteria, algae, and protozoans that cause diseases in humans, other animals or plants. As a result of pathogens from polluted stormwater runoff, Port Jefferson and Mt. Sinai Harbors are listed as Impaired Waterbodies on the NYSDEC’s Section 303(d) list.

Do Not Feed Wild Waterfowl

Do Not Feed Wild Waterfowl – Waterfowl are wild birds that can locate natural food sources throughout the year. Learn about why supplemental feeding by people is unnecessary and potentially harmful to waterfowl.


There are many ways in which the things we do impact our stormwater. Illegal sanitary sewer connections, damaging or changing stormwater drains or pipes, and dumping materials into stormwater drains are some of the intentional actions that can pollute our stormwater systems. Other activities also result in polluted stormwater that may not be so obvious, such as discharging chlorinated pool water to roadways or storm drains, using pesticides and herbicides on our lawns and gardens, not properly cleaning up automotive fluids on outdoor impervious surfaces, and changing vegetated areas to pavement or concrete. Learn about ways to reduce stormwater pollution in the Publications and Materials section of this website.

Residents can help prevent pollution by properly disposing of all materials, and clean up pollution by participating in beautification projects and beach clean-up events.

The municipal employees that monitor the stormwater program cannot be at all places at all times. Residents are encouraged to report questionable activities related to stormwater pollution. A local law is in place that prohibits discharging of unauthorized materials into storm systems. Please fill out theIllicit Discharge Reporting Form or contact a Village Code officer to report any activity that may be impacting a storm sewer system.

Another local law is in place that requires construction companies to protect storm sewer systems while performing their work. The Construction Activity Reporting Form may be used, or contact a Village Code officer, to report any construction activities that do not have barriers or treatment in place to stop construction materials or soils from entering the storm drain system.


The Village of Port Jefferson is seeking information from residents and businesses with respect to their understanding of stormwater related issues in the community. In order to better understand what the Village must do to better inform residents and businesses, we ask that you complete the following short questionnaire and return it to us either electronically (by clicking the submit button at the bottom of the form) or in hard copy. Hard copies may be hand delivered to Village Hall or mailed to: Stormwater Management Coordinator, c/o Village Clerk, Incorporated Village of Port Jefferson, 121 West Broadway, Port Jefferson, NY 11777.

Stormwater Questionnaire


  • To report a Stormwater / Water Quality concern such as: Dumping into a drain, Wastewater discharge into a storm drain, Complaint of illegal dumping into the storm sewer system or waterway, or Stormwater runoff containing soil/silt from a construction site draining into the street or a waterway:
  • Please call Village Code at (631) 774-0066 or complete either the Illicit Discharge Reporting Form or Construction Activity Reporting Form. The form can be dropped off or mailed to Village Hall (Stormwater Management Coordinator, c/o Village Clerk, Incorporated Village of Port Jefferson, 121 West Broadway, Port Jefferson, NY 11777) or e-mailed to
  • To report a drainage issue (flooded street, storm drain filled with sand/silt) please call the Department of Public Works at (631) 473-4733.
  • General questions or comments about this site or stormwater can be sent to:

Stormwater FAQ

Q. Where does the storm drain go?
A. Water that flows down roads, streets, and parking lots goes into a storm drain. Some drain into a leaching pool structure or recharge basin (sump), which then leaches into the ground. Other storm drains in the downtown area flow directly to Old Mill Creek or Port Jefferson Harbor.

Q. What is the purpose of the storm drain system?
A. Its purpose is to prevent flooding of roads and parking lots by quickly and efficiently transferring rain water into the ground or to Port Jefferson Harbor.

Q. Why are we stenciling or adding markers to storm drains with a message?
A. Storm drain stenciling and marking are a great way to remind people that storm drains are for clean rain water only. It is a visual reminder not to dump garbage or pollutants into the storm drains since these may end up in Port Jefferson Harbor.

Q. What’s the difference between putting water down the storm drain and putting water down the toilet or sink?
A. The sanitary sewer (toilets and sinks) and storm drain system are two completely different systems. The water that goes down sinks or toilets in homes and businesses flows to the sewage treatment plant on the west side of Port Jefferson Harbor, where it is treated before its release to the Harbor. Water that flows down roads, streets, and parking lots in the downtown area flow directly to the Harbor. This water picks up garbage pollutants along the way and does not receive any treatment to remove pollutants.

Q. Who fixes clogged storm drains?
A. The Village of Port Jefferson Highway Department at 631-473-4733.

Q. Why shouldn’t yard trimmings and soil go into the storm drain?
A. When natural materials, such as yard trimmings, break down, oxygen is drawn from the water. A lot of natural debris decomposing in water will deplete the water of oxygen needed by fish.
In addition, pesticides, oil leaked onto roads, pet waste, and other pollutants are scoured from all paved surfaces throughout our Village and are washed ultimately into Port Jefferson Harbor.

Q. Why isn’t storm water treated before it goes into Old Mill Creek or the Harbor?
A. Each storm drain goes to one of the twenty outfalls that discharge to Old Mill Creek or Port Jefferson Harbor. As a result, storm water is not collected into one location where it can be cleaned. Preventing pollution at the source is a much more effective and less costly way to prevent storm water pollution.

Q. What do I do if I see someone dumping something other than rain water down a storm drain?
A. Call Code Enforcement at 631-774-0066.

Q. What do I do if I see water and mud flowing from a construction site onto the street?
A. Call the Building Department at 631-473-4744.

Q. If I leave a complaint, will my name and address be kept confidential?
A. Yes, all information will be kept confidential.