Pathogen Contamination

The Problem

Human exposure to pathogens can cause illness, most often gastroenteritis, but also potentially more serious diseases such as salmonellosis and hepatitis A. Exposure to pathogens can occur either by direct contact with, or ingestion of, contaminated waters by bathers or by eating raw or partially cooked shellfish harvested from contaminated waters. Indications of pathogen contamination have resulted in closed beaches and shellfishing areas, hurting the economy of the region and damaging public perception of the quality of the Sound and its resources.

Pathogen contamination regularly causes a number of beach closures around the Sound.

  • From 1986 to 1990, the Management Conference identified 10 beaches that were chronically closed (defined as closed for at least three days per year for at least three of the five years) to swimmers due to pathogen contamination. The chronically closed beaches, in order of severity, were Scudder Park, Gold Star Battalion, Mamaroneck Area, Huntington Beach Community, Hempstead Harbor Area, Centerport Yacht Club, Fleets Cove, and Mamaroneck Beach Cabana and Yacht Club in New York and the beaches in the Norwalk and Milford areas of Connecticut.
  • Almost all closures occurred at beaches in embayments, rather than directly on the Sound, because of proximity to sources and reduced flushing.

Many productive shellfish beds are also closed due to pathogen contamination.

  • In New York, of the 66,000 acres of productive shellfish beds, 73 percent were either completely closed to shellfishing or subject to significant harvest limitations in 1990. Despite these restrictions, the proportion of Long Island Sound hard clams relative to the total harvest from all New York waters has gone from 4 percent in 1972 to 36 percent in 1991. This is due to increased shellfish production in the Sound and reduced hard clam harvests in the southern bays of Long Island (i.e., Great South Bay, Moriches Bay, etc.). Most of the hard clams were harvested from the townships of Huntington and Oyster Bay.
  • In Connecticut, of the 52,500 acres of productive shellfish beds, 35 percent were either completely closed to shellfishing or subject to significant harvest limitations in 1990. Approximately 85 to 90 percent of the harvest of Connecticut oysters and clams from approved waters was originally relayed or transplanted from restricted and prohibited areas by the shellfish industry. This creates additional costs to the industry.

The Cause of the Problem

Pathogens in Long Island Sound originate from untreated or inadequately treated human sewage and wild and domestic animal wastes. They enter the Sound from point and nonpoint discharges.

On an annual average basis, the estimated percent of fecal coliforms (an indicator of pathogen contamination) discharged into Long Island Sound from different sources are:

  • 51.6 percent from rivers, which includes upstream point (e.g., sewage treatment plants) and nonpoint sources (e.g., failing septic systems);
  • 47.3 percent from urban runoff, which includes combined sewer overflows; and
  • 1.1 percent from sewage treatment plants and industrial sources discharging directly to the Sound.

However, short-term discharges that are small on an average annual basis, such as discharges from vessels, can be significant sources in localized areas.

In New York state, rainfall causing combined sewer overflows and stormwater runoff was the primary cause of beach closures during the 1986 to 1990 review period. In Connecticut during that period, sewage treatment plant malfunctions were the primary cause of beach closures.

In both Connecticut and New York, the primary cause of shellfish bed closures varied from harbor to harbor but appeared to be primarily caused by nonpoint source pollution, especially from stormwater runoff. In harbors where detailed case studies were conducted, stormwater runoff, failing septic systems, and boats and marinas appeared to contribute to pathogen-related closures. Sewage treatment malfunctions may also have been significant on a local basis. Some of these closures are administrative or precautionary closures, while others are based on ambient data.

The Plan to Solve the Problem

The Management Conference recommends that management actions be taken to control the major sources of pathogens and that site- specific management plans for each harbor, embayment, or discrete shellfish bed area be developed and implemented. This can be best accomplished by directing priority attention at four source control categories in the following order: combined sewer overflows, nonpoint source runoff, sewage treatment plant malfunctions, and vessel discharges. Those and other sources of pathogens should be identified by conducting site-specific surveys leading to better control of local sources of pathogens.

Combined Sewer Overflows

  • New York City has begun to implement a combined sewer overflow abatement program to control the discharge of pathogens at a cost of $1.5 billion with enforceable completion dates for various aspects of the program during the period of 2001 to 2006.
  • Connecticut will implement its long-term combined sewer overflow abatement program to manage combined sewer areas that affect Long Island Sound. The cities of Norwalk, Jewett City, Derby, Norwich, and Shelton have combined stormwater and sanitary systems that will be corrected by the year 2000 at a cost of approximately $27 million. Bridgeport and New Haven have large systems that will be corrected in phases. The first phases are underway with remaining phases scheduled over the next 20 years at costs of $91 million and $125 million, respectively

Nonpoint Source Runoff

  • New York and Connecticut are implementing general statewide stormwater permit programs to manage stormwater from industrial and construction activities, in accordance with the EPA’s national program regulations. These permits regulate construction activity at sites greater than five acres and from 11 industrial categories.
  • New York state has initiated a pilot program using enforceable instruments (e.g., permits or consent agreements) to control and manage stormwater that causes closures of bathing beaches and shellfish beds. This pilot program has been funded at a cost of $100,000. Based on the program’s effectiveness, more widespread implementation will be considered.
  • Connecticut and New York commit to using their statewide nonpoint source programs and to developing coastal nonpoint pollution control programs to control pathogen discharges to Long Island Sound. Successful implementation of these programs is contingent upon fully funding the nonpoint source control programs under Section 319 of the Clean Water Act and Section 6217 of the Coastal Zone Act Reauthorization Amendments.

Sewage Treatment Plant Malfunctions

  • The EPA and the states of Connecticut and New York agree to take immediate enforcement seeking corrective actions and penalties in cases where sewage treatment plant malfunctions result in closures of bathing beaches or shellfish beds.
  • Connecticut and New York commit to taking timely enforcement to eliminate dry weather overflows, eliminate illegal hookups to storm sewers, and to control wet weather overflows from sewers caused by excessive infiltration and inflow, especially in areas near bathing beaches and shellfish growing waters.

Vessel Discharges

  • The states of Connecticut and New York will identify specific embayments warranting protection from vessel sewage discharge beyond the protection offered through the federal marine sanitation device standards and, to the extent feasible, will designate these embayments as no discharge zones after the EPA has determined that there are adequate pumpout and treatment facilities.
  • New York state has identified Huntington and Lloyd Harbors as areas requiring additional protection and the EPA has issued an official public notice of its tentative determination that adequate pumpout or treatment facilities exist in the areas. Assuming a final affirmative determination, the NYSDEC will designate Huntington and Lloyd Harbors as the first no discharge zones in Long Island Sound.
  • New York and Connecticut have received $1 million and $120,000 respectively in Clean Vessel Act grants to install vessel sewage pumpout facilities in Long Island Sound and other coastal waters. Both states will apply for additional funds in fiscal years 1995- 97 to meet the need for pumpout facilities in harbors and embayments identified as potential no discharge areas.

Site-specific Surveys

  • The states of Connecticut and New York will continue to perform bacterial surveys of harbors and embayments to identify contaminated shellfish areas and potential sources of pathogens. The states will continue to use seasonal or conditional certification of shellfish harvest areas and will act to open or close shellfish beds or bathing beaches, as may be warranted by water quality conditions.
  • The Management Conference recommends that each state perform surveys to assess the impacts of point and nonpoint sources of pathogens and to identify management options. Management actions should be identified based on viability of the resource and feasibility and cost-effectiveness of management. New funding of $300,000 per year is needed to implement this recommendation at the rate of two harbors per state per year.


With reductions in the major sources of pathogens that cause water quality or health-related problems in the Sound, existing shellfish beds and bathing beaches will be further protected and, where feasible, impaired bathing beaches and shellfish beds will be opened. This will help ensure protection of public health while minimizing negative effects on the regional economy caused by bathing beach and shellfish bed closures.

Costs and Funding

Successful implementation of this plan is contingent upon the states receiving, at a minimum, level funding for existing programs associated with pathogen assessment and control.

Two significant program enhancements have already been funded. A $100,000 pilot program was initiated in New York to use enforceable instruments to control and manage stormwater. Connecticut and New York have received $120,000 and $1 million, respectively, in Clean Vessel Act grants to install vessel sewage pumpout facilities in Long Island Sound and other coastal waters.

New funding of $150,000 per year per state is needed to implement surveys for sources of pathogens and develop site-specific management actions.

The cost of implementing long-term combined sewer overflow abatement programs is estimated to cost $243 million in Connecticut and $1.5 billion in New York. Adequate capitalization of the State Revolving Fund program in each state is required to fund these efforts.

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