Nonpoint source pollution presently degrades the quality of ground and surface waters in the South Shore Estuary Reserve. Nonpoint source pollution generally results from stormwater runoff, precipitation, atmospheric deposition, drainage, seepage and modifications to waterways. In the Reserve it poses potential hazards to human health, causes the periodic closure of bathing beaches, and has forced the closure of approximately 34,643 acres of hard clam beds in the Reserve, about one-third of its total area [Technical report: Nonpoint Sources of Pollution (1998)].

The dominant effect of nonpoint source pollution on water quality in the Reserve is well documented. The NYS Department of Environmental Conservation has identified polluted stormwater runoff from urban areas -- from new and existing development and from roads, highways, and bridges -- as the primary pollutant responsible in nearly all of the fifty-one South Shore Estuary Reserve waterbody segments listed with impaired uses in its 1996 Priority Waterbody List (see map at end of this chapter). Furthermore, when the Department updated its 1991 Priority Waterbody List in 1996, only one waterbody segment in the Reserve had improved in water quality while two were added to the list and seven others had their use impairments worsen [Technical reports: Nonpoint Sources of Pollution (1998); Status and Trends (1999)].

At least five reports, the first dating from 1978 -- the 208 Areawide Waste Treatment Study, Long Island Segment of the Nationwide Urban Runoff Program, Nonpoint Source Handbook, Nonpoint Water Quality Strategy for Nassau County, and Suffolk County Water Quality Strategy - - concluded that nonpoint source pollution was a priority concern and that, in particular, polluted stormwater runoff was the primary source. Each of these reports sets forth recommendations to control nonpoint source pollution. These recommendations, however, were never fully implemented.

Point sources of pollution - typically discrete and discernible pipe outfalls - also exist within the Reserve, and are regulated and monitored through the State Pollution Discharge Elimination System (SPDES) permit program. Point sources of pollution, while not as widespread and comparatively less significant than nonpoint sources, can still cause water quality degradation in their immediate areas. Such point sources include five wastewater treatment plants (Bay Park, Long Beach, West Long Beach, Lawrence, Jones Beach) that discharge treated effluent into the western bays; the Ocean Beach plant, discharging into Great South Bay; and the Village of Patchogue plant that discharges into the Patchogue River. Point sources also include other discharges regulated by SPDES and inactive hazardous and inactive and active solid waste disposal sites [Technical report: SSER State Pollution Discharge Elimination System (SPDES) Permit Sites (1999)].

In keeping with Article 46 of Executive Law, the Council established as one of its goals the need to "achieve and maintain the water quality necessary to preserve and rehabilitate resources of the estuary." Attaining this ambitious water quality goal depends upon the cooperative efforts of many players -- federal, State, and local governments, non-governmental organizations, resource users and residents. This chapter offers a fundamental approach to guide public and private efforts in the achievement of this goal. Recommendations in this chapter provide for the implementation of a strategy to control nonpoint source pollution and to further evaluate the effects of point sources. These recommendations are intended to guide the actions of governments seeking to improve water quality in the estuary.

Two of the most significant pollutants in the South Shore Estuary Reserve are elevated levels of coliform bacteria and excessive concentrations of certain nutrients. Coliform bacteria are typically found within the digestive systems of warm-blooded animals and indicate the potential presence of fecal wastes in surface waters. Coliform bacteria from wildlife, waterfowl and pet wastes and potentially from failing on-site wastewater treatment systems enter streams and coastal waters primarily through stormwater runoff from lawns, roads and parking lots. Elevated levels of coliform bacteria are responsible for the closure of shellfish beds and bathing beaches due to potential threats to human health [Technical report: Nonpoint Sources of Pollution (1998)].

As nonpoint source pollution originates from land use and water-based human activities, the Council's strategy calls on municipalities within the Reserve to assume a leadership role in reducing and controlling nonpoint pollution by exerting their legal authority to influence such activities, and preserving high quality waters from future pollution. The strategy presents corrective and preventive actions that local governments can take, supported by State and federal programs and grants and augmented by the efforts of non-governmental organizations, to reduce and control nonpoint source pollution.

The strategy's corrective and preventive measures fall into four management approaches: 1) identifying opportunities and developing schedules to protect lands that provide significant pollutant abatement functions; 2) designing and undertaking projects that retrofit existing storm sewer and other conveyance systems to remove pollutants carried by stormwater; 3) adopting nonpoint source pollution best management practices; and 4) increasing education and outreach to modify resident and user behavior. The degree to which each of the four approaches may be institutionalized in a municipality will depend upon local circumstances.

Several steps are fundamental to the implementation of the corrective component of the strategy. First, the distribution and relative magnitude of nonpoint source pollution in each watershed should be identified by municipalities. Satellite imagery of land cover has been used with soils, topography and distance to surface water data to identify nonpoint pollution potential for the entire Reserve (see map at end of this chapter). This information will help focus implementation of site-specific stormwater remediation projects and water quality monitoring efforts.

Next, municipalities should characterize their watersheds. These characterizations should include a delineation of sub-watersheds or contributing areas, and the location and condition of storm sewer outfalls and stormwater conveyance systems through which pollutants in stormwater are discharged. Existing drainage and runoff patterns should be accounted for in this delineation.

An assessment of the likelihood of correcting discharge problems through infrastructure retrofit improvements should also be included. The likelihood of improvement and value of the receiving water resources are two key factors to be considered in setting priorities and are essential to preparing watershed management plans, a follow-up step that would establish the basis for the design of cost-effective corrective projects. Environmental Protection Fund Local Waterfront Revitalization Program grants are available to assist in this phase of the process. For example, as part of its stormwater abatement program, the Town of Southampton has inventoried and mapped potentially significant contributing areas, assessed nonpoint pollution and identified capital improvement projects to abate pollution. It has also identified other areas to be analyzed as future target areas. Brookhaven has identified outfalls and conveyance systems that discharge to tidal tributaries in the town and developed preliminary recommendations to remove pollutants. Babylon has identified outfalls, contributing areas and projects to remove pollutants in runoff and restore wetlands for its Ketchams Creek watershed. Nassau County has mapped stormwater drainage areas and outfalls, while Hempstead has identified catchment basins and retention structures for all of its roads. Inventories in Oyster Bay and Islip are still underway.

Previous actions to control point sources of pollution within the Reserve have focused on pollutant loads from private sources and on upgrades to wastewater treatment plants. There is also ongoing remediation of inactive hazardous waste and solid waste disposal sites, cleanup of spills in waterbodies, identification of areas of potentially contaminated sediments, and regulation of discharges through the State Pollution Discharge Elimination System permit program. Future efforts should focus on exploring potential impacts of point sources relative to one another and to nonpoint sources, and the remediation, when feasible, of areas where point sources of pollution have caused documented impairments to designated uses and/or living resources [Technical reports: State Pollution Discharge Elimination System (SPDES) Permit Sites (1999); Inactive Hazardous Waste Disposal Sites and Active and Inactive Solid Waste Disposal Facilities (1999); Areas of Contaminated Sediments (1998)].

Surface water quality data in the South Shore Estuary Reserve is collected on a regular basis by the NYS Department of Environmental Conservation under its Rotating Intensive Basin Study and shellfish certification program, and by the U.S. Environmental Protection Agency, the National Park Service, the Suffolk County Department of Health Services, the Town of Hempstead and other municipalities, several citizen monitoring groups and colleges. Groundwater resources in the Reserve are monitored by the U.S. Geological Survey [Technical report: Coordinated Water Resource Monitoring Strategy for the South Shore Estuary Reserve (1999)].

The coordination of these activities is described in the Coordinated Water Resource Monitoring Strategy for the South Shore Estuary Reserve (1999). This study recommends a comprehensive and coordinated strategy that focuses on multiple objectives beyond corrective efforts for nonpoint source pollution control. These objectives were drawn from the Council's overall goal to protect and restore the estuary, and include: 1) management of hard clams; 2) control of coliform bacteria in stormwater and maintenance of shellfish areas; 3) control of brown tide; and 4) maintenance and restoration of the natural system. The strategy evaluated the diverse monitoring programs already in place and identified gaps in existing information and approaches. It is a multi-tiered approach, with a baseline monitoring program proposed as a first tier, and a second tier that calls for hypotheses-driven sampling that would address chemical loading, water quality, and ecological integrity. The strategy: proposes that physical, chemical, biological and human-induced parameters be tracked; identifies general locations and frequency of sampling, including the rationale for such sampling; and provides cost estimates. Human-induced parameters include land use changes, sewering and on-site wastewater treatment systems, land application of toxins and fertilizers, resource harvest, recreational boating and inlet control. The coordinated monitoring strategy also recommends that historical water quality data be analyzed in order to establish baseline conditions for the Reserve's tributaries and bays.

The Council offers the following recommendations to achieve and maintain water quality in the South Shore Estuary Reserve. In an effort to reduce and control nonpoint source pollution, recommendations 1 through 13 call for corrective actions in the form of remediation projects to manage storm water as it moves across the landscape and preventive actions that control the level of pollutants that enter stormwater runoff and the Reserve's bays and tributaries. Many of these preventive actions involve the implementation of best management practices by municipalities in the Reserve. In an effort to address point sources of pollution, recommendations 14 through 17 call for enhancements to existing source controls. Recommendations 18 through 21 relate to the Environmental Protection Agency's Storm Water Phase II Final Rule. Recommendations 22 through 24 identify information gaps that need to be addressed within the next three years in order to move toward fulfillment of the Council's vision for Long Island's South Shore Estuary Reserve.

1. Complete assessments of nonpoint source pollution management practices and identify and implement needed preventive measures based on priorities.

The six towns and two counties in the Reserve have already completed assessments of their current nonpoint source pollution control practices. Villages in the Reserve, the City of Long Beach, and relevant State agencies should conduct similar assessments of their nonpoint control practices and identify gaps in those practices. Towns should consider assisting villages within their borders with the completion of such assessments.

Comprehensive spatial analysis of land cover, soils and topography by the NYS Department of State has resulted in a nonpoint pollution potential model (see map at end of this chapter). The model identifies the potential distribution and relative magnitude of nonpoint source pollution and should be used by municipalities as they develop watershed plans that address management of nonpoint source pollution.

A watershed analysis involves identifying and setting priorities for improvements to storm sewers and other runoff conveyance systems. It should also: examine the overall watershed character, including existing drainage and runoff patterns; evaluate the benefits and feasibility of correcting runoff problems through road infrastructure improvements; and identify opportunities for preservation of high quality waters from future pollution. This information could be supported with data from targeted water quality monitoring programs. Such watershed analyses have been conducted in whole or in part by Southampton, Brookhaven, Babylon, Hempstead and Nassau County, and are underway in Islip and Oyster Bay. Similar work needs to be done, where appropriate, by Suffolk County and by New York State, particularly the NYS Department of Transportation, regarding State highways, and the NYS Office of Parks, Recreation and Historic Preservation, regarding major park holdings.

Based on the results of watershed analyses, watershed plans should identify significant nonpoint source contributing areas and identify and set priorities for site-specific projects for stormwater remediation. Designs for these projects should be developed according to the practices from either the Environmental Protection Agency's Guidance Specifying Management Measures for Sources of Nonpoint Pollution in Coastal Waters or the NYS Department of Environmental Conservation's Management Practices Catalogue for Nonpoint Source Pollution Prevention and Water Quality Protection in New York State. The latter is incorporated by reference into the New York State Coastal Nonpoint Pollution Control Program, a compendium of nonpoint pollution control and abatement practices currently implemented in New York State.

Stormwater remediation projects can be implemented through a mix of local resources, such as general funds, capital improvements programs, special bond initiatives, or municipal work crews, and State funding mechanisms such as the 1996 New York State Clean Water/Clean Air Bond Act and the Environmental Protection Fund. In some instances, federal dollars may be available to fund projects through the Transportation Enhancement Act (TEA-21), section 319 of the federal Clean Water Act, and through the proposed authorization for the Coastal Nonpoint Source Pollution Control Program.

A system of reporting to the Council by municipalities should be established to measure Reserve-wide progress against objectives, and to enable early detection and resolution of Reserve-wide problems. The Council could also serve as a clearinghouse of information and techniques that would be shared with individual South Shore Estuary Reserve municipal stewards.

In an effort to reduce levels of hazardous and toxic substances associated with construction activities from contaminating stormwater runoff, Southampton, Hempstead and Babylon should incorporate into their site plan review regulations, and Nassau County into its subdivision regulations, management practices that: 1) control erosion and sedimentation before and during site preparation and construction; and 2) minimize detrimental effects on the water quality of waterbodies before and during site preparation and construction. These practices are found in NYS Department of Transportation design specification documents and the NYS Department of Environmental Conservation's Management Practices Catalogue for Nonpoint Source Pollution Prevention and Water Quality Protection in New York State; the former document is also incorporated by reference in New York State Coastal Nonpoint Pollution Control Program. Additionally, all towns should immediately ensure that their land use regulations address construction activities that disturb from one to less than five of acres of land in advance of the permit conditions that will be required by the Environmental Protection Agency's Final Storm Water Phase II Rule.

To reduce the significant water quality impacts of stormwater runoff from existing roads, highways and bridges, all towns in the Reserve should formally adopt roadway operation and maintenance practices from portions of NYS Department of Transportation procedural manuals and NYS Department of Environmental Conservation's Management Practices Catalogue for Nonpoint Source Pollution Prevention and Water Quality Protection in New York State.

To reduce the impacts caused by stormwater runoff contaminated by activity-specific nonpoint sources of pollution, the following practices should be instituted:

1) To mitigate and prevent spills of petroleum products and hazardous materials, all towns in the Reserve should: a) incorporate standards from the National Fire Protection Association and Environmental Conservation Law Article 27 for generation, storage, application, handling and disposal activities before, during and after site preparation and construction into site plan review regulations, and local law; b) incorporate U.S. Occupational Safety and Health Administration standards and procedures pertaining to spill cleanups into site plan review regulations, subdivision requirements and local law; and c) train an emergency spill response team in these standards and procedures.

2) To address excessive fertilizer, herbicide and pesticide use as part of management of turf grass in public and private areas, all towns in the Reserve should educate citizens, contractors, construction workers, and owners and managers of private facilities on the importance of carrying out best management practices, including soil testing, use of integrated pest management, organic gardening and lawn care.

3) To reduce the amount of wildlife and pet wastes entering waterbodies, Babylon, Hempstead and Southampton should undertake multi-component education programs that discourage the feeding of waterfowl, and Brookhaven and Southampton should institute "pooper-scooper" laws.

To reduce elevated levels of fecal coliform bacteria and toxic substances associated with existing marinas, all towns in the Reserve should incorporate into local law practices from the NYS Coastal Nonpoint Pollution Control Program, the NYS Department of Environmental Conservation Management Practices Catalogue for Nonpoint Source Pollution Prevention and Water Quality Protection in New York State and the National Fire Protection Association Fire Protection Standard for Pleasure and Commercial Motor Craft. Such efforts should include adoption of appropriate regulations and practices that mitigate the impacts of vessel waste discharges. The imposition of best management practices on private marinas should be balanced against the provision of incentive subsidies such as tax relief and public funding for rehabilitation.

All Reserve towns except Southampton need to target outreach efforts at marina patrons in an effort to reduce solid waste reduction and encourage recycling, while all towns except Babylon need to target outreach efforts on fish cleaning practices at sites designated for that purpose.

To reduce levels of fecal coliform bacteria and toxic substances associated with new marinas, all towns in the Reserve should incorporate siting and design practices from the NYS Coastal Nonpoint Pollution Control Program and the NYS Department of Environmental Conservation Management Practices Catalogue for Nonpoint Source Pollution Prevention and Water Quality Protection in New York State into site plan review.

These practices should be applied to new and expanding private marinas and to public marinas through formally adopted planning approval procedures. The imposition of these practices on private marinas undergoing redevelopment should be balanced against the provision of incentive subsidies such as tax relief and public funding for rehabilitation.

To reduce the water quality impacts of existing hydromodification activities, all towns in the Reserve should adopt into local operation and maintenance procedures those practices from the NYS Department of Environmental Conservation Management Practices Catalogue for Nonpoint Source Pollution Prevention and Water Quality Protection in New York State for restoring and creating wetlands. All towns except Southampton need to adopt those practices from the catalogue that address improvements to stream corridors and the restoration of riparian habitat and vegetation.

To prevent the water quality impacts of new private hydromodification activities, all towns in the Reserve should incorporate into their site plan review, and Nassau County into its subdivision regulations, practices from NYS Department of Transportation design specification documents and the NYS Department of Environmental Conservation Management Practices Catalogue for Nonpoint Source Pollution Prevention and Water Quality Protection in New York State to protect wetlands and streams, and control erosion and sedimentation before and during site preparation and construction. These practices also should be formally adopted into local operation and maintenance procedures and applied to municipal hydromodification activities as well.

All towns also should formally adopt into local operation and maintenance procedures those practices from NYS Department of Transportation procedural manuals and NYS Department of Conservation's Management Practices Catalogue for Nonpoint Source Pollution Prevention and Water Quality Protection in New York State that address the clearing of debris from streams and culverts.

To reduce the water quality impacts of on-site wastewater treatment systems, Nassau and Suffolk counties should work with Hempstead, Babylon, Islip and Brookhaven to develop and implement on-site system management strategies that include a regulatory and incentive program for periodic inspections and pumpouts of OWTS, require upgrades of OWTS as part of substantial residential and commercial redevelopment, and establish a public education component that informs system owners of proper use and the maintenance necessary for proper operation. Southampton should institute a similar public education program.

The Town of Brookhaven should enforce those provisions of its town code that address new and replacement systems in special flood areas and that establish design criteria for systems in coastal high hazard areas. Southampton should fully implement those provisions of its town code that require inspections of systems at five-year intervals and remediation as necessary, amend those provisions to allow inspections by private individuals certified by the Town, and establish such a certification program. Additionally, Southampton should extend its requirement of OWTS upgrades whenever wetland permits are issued for expansions and additions to commercial establishments.

The Council offers the following recommendations to address actual and potential point source pollution. The recommendations are based on, respectively: a water quality initiative provided for in the federal Clean Water Act; comments from Council members; and completed South Shore Estuary Reserve technical reports. Implementation of these actions will take the concerted effort of State, federal and local governments.

14. Determine point and nonpoint source controls to reduce loadings of pathogens, nutrients and toxic substances contributing to water quality problems in the Reserve's tributaries and bays.

In order to determine point and nonpoint source controls necessary to address water quality problems associated with nutrient enrichment, pathogens or toxic substances, a systematic and sequential process must be followed. First, water quality data in the Reserve's tributaries and bays must be evaluated. Based on this evaluation, the NYS Department of Environmental Conservation will identify any specific waterbodies that should be included on its 303(d) list of impaired waterbodies that require the development of Total Maximum Daily Loads. In accordance with recently promulgated federal regulations, the next 303(d) list is expected to be finalized in April 2002. Later, for those waterbodies identified on the 303(d) list, the Department of Environmental Conservation will develop Total Maximum Daily Loads (TMDLs) in accordance with the schedule included in the list. TMDLs will identify reductions in point and nonpoint sources of pollutants necessary to meet water quality standards. Finally, the Department of Environmental Conservation, the Department of State, the Council and local governments should work together to implement any load reduction actions identified in the TMDL allocations.

Five wastewater treatment plants discharge secondarily treated effluent into the western bays. TMDL wasteload allocations for the waterbodies receiving discharges from these facilities should be used to determine whether upgrades of the municipal wastewater plants to tertiary treatment are necessary.

The compliance of point source discharges into the Reserve with current SPDES limits and conditions should be investigated. Based on the results, existing and future infrastructure or operational needs necessary to ensure compliance should be identified. The NYS Department of Environmental Conservation, the Department of State, the Council and local governments should then work together to assure that the needs identified are met.

National Fire Protection Association and Environmental Conservation Law Article 27 standards regulate hazardous waste generation, storage, application, handling and disposal activities before, during and after site preparation and construction. Practices in previously cited documents are designed to manage nonpoint source pollution. Areas of contaminated sediments that potentially impair waterbodies in the Reserve should be tested to determine required actions, and, if necessary, should be remediated on a priority basis when funding becomes available.

18. The NYS Department of Environmental Conservation should designate as "urbanized areas" under the Environmental Protection Agency's Storm Water Phase II Final Rule those portions of the Reserve not so designated by the Bureau of Census.

The Phase II Final Rule requires nationwide coverage of all small municipal separate storm sewer systems that are located within the boundaries of a Bureau of Census-defined "urbanized areas" based on the latest decennial Census. All of Nassau County has been designated as an "urbanized area." It is anticipated that most of the Suffolk County portion of the Reserve also will be designated as "urbanized areas" based on Census data. The NYS Department of Environmental Conservation, as the permitting authority, should ensure that this stormwater management program applies throughout the entire Reserve by designating those parts of the Reserve not considered "urbanized areas" on the basis of Census figures.

The National Pollution Discharge Elimination System permitting authority (the NYS Department of Environmental Conservation) will issue general permits for Phase II designated small municipal separate storm sewer systems and small construction activity by December 9, 2002. Designated municipalities must obtain permit coverage within 90 days of permit issuance. The permitting authority may phase in coverage for municipalities with populations under 10,000 on a schedule consistent with a State watershed permitting approach. Permitted municipalities must fully implement their stormwater management programs by the end of the first permit term, typically a five year period. Permit conditions will include at least six program elements: public outreach and education; public participation and involvement; illicit discharge detection and elimination; construction site runoff control; post-construction runoff control; and pollution prevention. All municipalities should immediately start the process to meet permit requirements. The implementation actions offered in this plan will help municipalities establish a foundation upon which to base their efforts at meeting the required permit conditions.

A cooperative information and education program will facilitate the timely implementation of the Phase II Final Rule by municipalities in the Reserve. Such a program should include: an overview of why the Phase II Storm Water Program is necessary; who is covered by the rule and what the rule requires to manage small municipal separate storm sewer systems and small construction activity; and the Phase II program approach, the schedule for implementation, and the Environmental Protection Agency's "tool box" of materials available to ensure that program implementation is effective and cost-efficient.

Implementation of the Phase II Final Rule will be the responsibility of counties, towns and villages in the South Shore Estuary Reserve. In an effort to address the reality of overlapping municipal authorities and to make implementation of the rule workable, the Departments of State and Environmental Conservation and municipalities in the Reserve should work together to identify optimal ways to develop stormwater management districts and explore the feasibility of those options.

22. Implement a coordinated water resources monitoring strategy that monitors water quality in the Reserve's tributaries and bays, and evaluates the extent to which management actions are successful in achieving water quality goals.

The Coordinated Water Resources Monitoring Strategy for the South Shore Estuary Reserve proposed a two-tiered program for monitoring the physical, chemical, biological and human-induced conditions of the Reserve and its watershed. Tier 1 monitoring is designed to establish baseline data on water quality in the Reserve's bays and tributaries, identify and assess trends in water quality, and evaluate the extent to which desired uses of the Reserve's water resources are met. Tier 1 efforts include monitoring the occurrence of brown tide blooms in the Reserve's waters. Tier 2 monitoring activities are in general short-term investigations, more intensive in temporal and /or spatial scale, and designed to test specific hypotheses regarding water quality or ecological issues in the South Shore Estuary Reserve.

The monitoring strategy builds on existing monitoring programs and offers recommendations for improved coordination among agencies conducting those programs. It calls for the hiring of a program manager, the implementation of a quality assurance/quality control program, and centralized data analysis and reporting.

Once strategic information is developed from the coordinated water quality monitoring program (Recommendation 22, above), a hydrodynamic model addressing groundwater underflow, tributary inputs, water circulation, currents, dispersion and residence times would add to the capability of refining and enhancing management strategies. Such a model would need to identify the potential hydrodynamic and water quality impacts, ecological consequences and long-term environmental fate of toxic substances, coliform bacteria, nutrients, and other pollutants to the bays to be of value. The model would be used to test the potential effects of alternative locations for wastewater outfalls and predict the water quality consequences of a storm-related island breach or inlet closure. Coupled with land use and water quality monitoring data through a GIS system, the model would be of use to local governments for understanding water quality impacts of alternative land use decisions.

Additional data are needed to further test the hypothesis that brown tide is related to inputs and the ratios of available dissolved organic nitrogen and dissolved inorganic nitrogen from groundwater, sediment nutrient flux, and other sources. Such research could also shed light on other ecological processes such as the influence of trace metals and pesticides. This research effort could also provide valuable information on conventional water quality and living resource management issues. Effective enhancement of hard clams, scallops, oysters, finfish, crustaceans, and submerged aquatic vegetation will be difficult until this harmful algal bloom is better understood.