Long Island South Shore Estuary Reserve 

Coordinated Water Resources Monitoring 

Strategy

Long Island

SOUTH SHORE ESTUARY RESERVE

New York

Nassau

Suffolk

Open-File Report 2017–1161

U.S. Department of the Interior

U.S. Geological Survey
Cover. The Long Island South Shore Estuary Reserve (orange) stretches west to east from the Nassau-Queens county line to the 

town of Southampton. South to north, it extends from mean high tide on the ocean side of the barrier islands to the inland limits of the 

watersheds that drain into the bays. Image courtesy of the New York State Department of State Office of Planning, Development and 

Community Infrastructure. 
Long Island South Shore Estuary Reserve 

Coordinated Water Resources Monitoring 

Strategy

By Shawn C. Fisher, Robert J. Welk, and Jason S. Finkelstein

Prepared in cooperation with the 

New York State Department of State Office of Planning, 

Development and Community Infrastructure and the 

South Shore Estuary Reserve Office

Open-File Report 2017–1161

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

RYAN K. ZINKE, Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2018

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U.S. Government.

Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials 

as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

Fisher, S.C., Welk, R.J., and Finkelstein, J.S., 2018, Long Island South Shore Estuary Reserve Coordinated Water 

Resources Monitoring Strategy: U.S. Geological Survey Open-File Report 2017–1161, 105 p., https://doi.org/10.3133/

ofr20171161.

ISSN 2331-1258 (online)
iii

Foreword

The original Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring 

Strategy (CWRMS), written in 2000, was part of a series of technical reports prepared 

as baseline information to support the creation of the 2001 South Shore Estuary Reserve 

Comprehensive Management Plan. This updated CWRMS, as noted in the executive summary, 

“provides an overview of the water-quality and ecological monitoring within the Reserve and 

presents suggestions from stakeholders for future data collection, data management, and 

coordination among monitoring programs.”

Many issues and challenges exist in the South Shore Estuary Reserve today that were not 

present or were not as extensive when the original CWRMS was written. Priority issues such 

as nitrogen and phosphorus pollution, low dissolved oxygen, bay-water acidification, harmful 

algal blooms, pathogens, sedimentation, microplastics, groundwater contamination from 

pharmaceuticals and personal care products, and fertilizer, pesticide, and herbicide pollution 

prompted the South Shore Estuary Reserve Council and the New York Department of State to 

create this updated CWRMS.

A series of group meetings, a public workshop, and individual meetings were held with 

members of the Project Advisory Committee (PAC). This PAC consisted of representatives of the 

New York State Department of State, the South Shore Estuary Reserve Council, the South Shore 

Estuary Reserve Citizens Advisory Committee, academia, watershed groups, environmental 

groups, the U.S. Environmental Protection Agency, the U.S. Fish and Wildlife Service, county soil 

and water conservation districts, the National Park Service, the U.S. Army Corps of Engineers, 

and the U.S. Geological Survey, who all made this updated strategy possible with their 

considerable experience and expertise in water-quality issues and monitoring protocols.

The New York State Department of State entered into a cooperative agreement with the 

U.S. Geological Survey New York Water Science Center to produce the 2017 CWRMS and 

coordinate the project. The USGS project staff included Christopher Schubert, Shawn Fisher, 

Robert Welk, and Jason Finkelstein; their expert technical qualifications and experience in 

water-quality, groundwater, and surface-water issues led to the production of this CWRMS.

It is our hope that the many stakeholders who are involved with water-quality and ecological 

monitoring efforts will find this document pertinent, useful, and timely as it relates to the issues 

that exist in today’s South Shore Estuary Reserve.

New York State Department of State/Office of Planning,

Development and Community Infrastructure and

The South Shore Estuary Reserve Office

v

Acknowledgments

Several of our colleagues at the New York State Department of State Office of Planning, 

Development, and Community Infrastructure provided valuable assistance, advice, and 

exceptional contributions to the content of this report. These colleagues include Nancy Rucks, 

Myra Fedyniak, Sherry Forgash, Lou Siegel, and Jeremy Campbell. Cooperation from the 

Long Island South Shore Estuary Reserve Council with support from the New York State 

Environmental Protection Fund is gratefully acknowledged.

vii

Contents

Foreword ........................................................................................................................................................iii

Acknowledgments.........................................................................................................................................v

Executive Summary.......................................................................................................................................1

Introduction.....................................................................................................................................................1

State of the South Shore Estuary Reserve .......................................................................................2

Current (2017) Management Topics...................................................................................................6

Eutrophication ..............................................................................................................................8

Managing Wastewater Infrastructure.....................................................................................8

Pathogens ...................................................................................................................................11

Total Maximum Daily Loads .....................................................................................................11

Harmful Algal Blooms ...............................................................................................................12

Wetland Loss ..............................................................................................................................12

Decline in Fisheries ...................................................................................................................13

Aquatic Vegetation Restoration ..............................................................................................13

Climate Change and Resiliency...............................................................................................13

Forcing Functions................................................................................................................................14

Trophic State Indicators ....................................................................................................................15

Low-Impact Development and Best Management Practices.....................................................17

Citizen Science....................................................................................................................................18

Synergy Among Existing Management and Action Plans ...........................................................18

Purpose and Scope ............................................................................................................................18

Resource Monitoring in the Long Island South Shore Estuary Reserve ............................................18

Water-Quality and Water-Quantity Programs................................................................................19

Continuous Water-Quality Monitoring....................................................................................19

Discrete Water-Quality Monitoring.........................................................................................25

Water-Quantity Monitoring ......................................................................................................26

Biological Monitoring and Surveys .................................................................................................27

Vertebrates and Invertebrates ................................................................................................27

Microalgae and Macroalgae...................................................................................................28

Wildlife.........................................................................................................................................28

Invasive Species........................................................................................................................28

Sediment-Quality Monitoring............................................................................................................28

Atmospheric Monitoring....................................................................................................................29

Quality Assurance and Quality Control, Metadata, and Data Archives .............................................29

Quality Assurance and Quality Control ...........................................................................................29

Quality Assurance Project Plans ............................................................................................30

Proposed Ranking of Data........................................................................................................30

Defining and Standardizing Metadata ............................................................................................31

Electronic Field Forms...............................................................................................................32

Metadata Database...................................................................................................................32

Standardizing the Archival of Data..................................................................................................32

Data Gaps and Specific Recommendations............................................................................................33

Water Resources ................................................................................................................................33
viii

Ecological Resources.........................................................................................................................39

Estuarine Dynamics............................................................................................................................40

Atmospheric Resources ....................................................................................................................41

Infrastructure and Land Use.............................................................................................................41

General and Coordination Recommendations From the Project Advisory Committee ....................42

General Recommendations of the Project Advisory Committee ................................................42

Recommendations for Stakeholder Coordination by the Project Advisory Committee ..........46

Coordinated Water Resources Monitoring Strategy Website .............................................................47

Resources and Data...........................................................................................................................47

Mapper.................................................................................................................................................48

Metadata Attributes ..................................................................................................................48

Functionality................................................................................................................................48

Potential Expansion...................................................................................................................48

References Cited..........................................................................................................................................50

Appendix 1. Updates to Recommendations Presented in the 2000 Coordinated Water 

Resources Monitoring Strategy...................................................................................................71

Appendix 2. New York State Department of Environmental Conservation 303(d) List of 

Impaired Waters.............................................................................................................................81

Appendix 3. Expanded List of Management Plans Created or in Progress for Resources 

Within the Long Island South Shore Estuary Reserve, New York..........................................89

Appendix 4. Members of the Project Advisory Committee for the Long Island South Shore 

Estuary Reserve 2017 Coordinated Water Resources Monitoring Strategy ........................93

Appendix 5. Notes From the South Shore Estuary Reserve Coordinated Water Resources 

Management Strategy Project Advisory Committee Meetings..............................................97

Figures

1. Map showing political boundary of the South Shore Estuary Reserve, Long Island, 

New York ......................................................................................................................................16

2. Map showing ongoing and proposed monitoring in the western bays of the 

South Shore Estuary Reserve, New York................................................................................20

3. Map showing ongoing and proposed monitoring in the Great South Bay of the 

South Shore Estuary Reserve, New York................................................................................21

4. Map showing ongoing and proposed monitoring in the eastern bays of the 

South Shore Estuary Reserve, New York................................................................................22

5. Screenshot of the South Shore Estuary Reserve Coordinated Water Resources 

Monitoring Strategy website mapper .....................................................................................49
ix

Tables

1. Constituents collected or proposed for monitoring of water or ecological resources

in the South Shore Estuary Reserve, New York.......................................................................3

2. Management plans for water or ecological resources in the South Shore Estuary

Reserve, New York .......................................................................................................................7

3. Management issues identified by the Project Advisory Committee for the South

Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy....................9

4. List of water-quality and ecological monitoring programs ongoing or completed since 

2000 in the South Shore Estuary Reserve, New York, with information on A, objectives 

and constituents and B, quality assurance and quality control, timeframes, and URLs ....

........................................................................................................................................................59

5. List of projects relevant to water quality and ecological health ongoing or completed 

since 2000 in the South Shore Estuary Reserve, New York.................................................23

6. Partial list of field equipment used or deployed for water-quality monitoring in the 

South Shore Estuary Reserve, New York................................................................................25

7. List of gaps in data collection programs identified and prioritized by the Project 

Advisory Committee for the Long Island South Shore Estuary Reserve Coordinated 

Water Resources Monitoring Strategy...................................................................................34

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

acre 0.4047 hectare (ha)

gallon per day (gal/d) 3.785 liter per day (L/d) 

inch per year (in/yr) 2.54 centimeter per year (cm/yr)

inch per year (in/yr) 25.4 millimeter per year (mm/yr)

Datum

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88) or the National Geodetic Vertical Datum of 1929 (NGVD 29).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Elevation, as used in this report, refers to distance above the vertical datum.
x

Abbreviations

BMP best management practice

CERCOM Center for Environmental Research and Coastal Oceans Monitoring

CMP Comprehensive Management Plan

CWRMS Coordinated Water Resources Monitoring Strategy

EPA U.S. Environmental Protection Agency

FEMA Federal Emergency Management Agency

FWS U.S. Fish and Wildlife Service

GIS geographic information system

GOSR Governor’s Office of Storm Recovery

GPS Global Positioning System

HAB harmful algal bloom

lidar light detection and ranging

LINAP Long Island Nitrogen Action Plan

LISS Long Island Sound Study

MS4 municipal separate storm sewer system

NOAA National Oceanic and Atmospheric Administration

NPS National Park Service

NWIS National Water Information System

NYS New York State

NYSDEC New York State Department of Environmental Conservation

NYSDOS New York State Department of State

PAC Project Advisory Committee

PAH polycyclic aromatic hydrocarbon

PCB polychlorinated biphenyl

PEP Peconic Estuary Program

PPCP pharmaceuticals and personal care products

QA/QC quality assurance and quality control

QAPP quality assurance project plan

SAV submerged aquatic vegetation

SCDHS Suffolk County Department of Health Services

SET surface elevation table

SoMAS Stony Brook University School of Marine and Atmospheric Sciences

SSER South Shore Estuary Reserve

STORET Storage and Retrieval
xi

TMDL total maximum daily load

TNC The Nature Conservancy

TSI trophic state indicator

USACE U.S. Army Corps of Engineers

USGS U.S. Geological Survey

WQX Water Quality Exchange

Long Island South Shore Estuary Reserve Coordinated 

Water Resources Monitoring Strategy

By Shawn C. Fisher, Robert J. Welk, and Jason S. Finkelstein

Executive Summary

The Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy (CWRMS) 

provides an overview of the water-quality and ecological 

monitoring within the Reserve and presents suggestions from 

stakeholders for future data collection, data management, 

and coordination among monitoring programs. The South 

Shore Estuary Reserve, hereafter referred to as the Reserve, 

is a 173-square-mile network of bays and tributaries shaped 

by the south shore of Long Island (New York) and the barrier 

islands that was formed as a result of the last ice age (roughly 

18,000 years ago). This overview and coordination document 

is based on information assembled from a series of meetings, a 

workshop, and individual correspondences with the CWRMS 

Project Advisory Committee, which was formed in 2015 to 

help guide the creation of the document, which reflects the 

current (2017) status of the Reserve and the need for additional data to address its water-quality issues and ecological 

health and to respond to a changing climate. The U.S. Geological Survey (USGS), in cooperation with the New York 

State Department of State Office of Planning, Development 

and Community Infrastructure and the South Shore Estuary 

Reserve Office, compiled information and recommendations 

to help stakeholders efficiently evaluate waters currently being 

monitored and address areas where necessary data are lacking. Water-quality monitoring in the Reserve is ongoing on 

the Federal, State, and local levels, and coordination among 

the various programs administered by the U.S. Environmental Protection Agency; National Oceanic and Atmospheric 

Administration; USGS; Shinnecock Tribal Nation; New York 

State; Nassau and Suffolk Counties; the Towns of Hempstead, 

Oyster Bay, Babylon, Islip, Brookhaven, and Southampton; 

and local universities and nonprofit organizations is necessary 

to ensure cooperation and efficient use of limited resources. 

Proper collection and archival of data are critical to the usability of data and methods—a sample of available repositories for 

monitoring data are provided in this report. Equally important are quality assurances of data and proper techniques of 

archival such that water and ecological data are collected and 

analyzed in a consistent manner, regardless of their sources, 

and that differences in methodologies are identified that might 

result in discrepancies in the compiled data. Details on monitoring programs, data gaps that are perceived by stakeholders 

and researchers in the area, and Project Advisory Committee 

recommendations are provided in this report to promote discussion and coordination. In most cases, resources to fill data 

gaps are needed, and the use of citizen science volunteers has 

been shown to help extend programs and provide insight into 

previously unaddressed areas of concern. This document, in 

conjunction with the CWRMS website and interactive mapper, 

is intended to inform the latest iteration of the Comprehensive Management Plan for the Reserve. Moreover, resource 

managers can use the CWRMS and mapper to identify areas 

of potential overlap and initiate conversations with stakeholders about addressing needs for additional monitoring of water 

quality and ecological health in the bays and tributaries of 

the Reserve.

Introduction

Since the Long Island South Shore Estuary Reserve Comprehensive Management Plan (CMP) was approved in 2001, 

much has been learned regarding the man-made and natural 

contributors that led to the impaired status of many of the bays 

and tributaries of the South Shore Estuary Reserve (hereafter 

referred to as the Reserve) in Long Island, New York. As a 

result, efforts are underway to improve ecological health and 

restore natural resources to the Reserve while improving its 

resiliency. The CMP lists objectives for the estuary system, 

including improving and subsequently maintaining water quality, restoring and protecting living resources, expanding public 

use and enjoyment, improving and sustaining the economy, 

community resiliency, and increasing education, outreach, and 

stewardship. These objectives are based on information that 

predates an increased frequency of algal blooms, two hurricanes, and the realization that groundwater is contributing 

most of the nutrients to the bays. The U.S. Geological Survey (USGS) and the New York State Department of State 

(NYSDOS) Office of Planning, Development and Community Infrastructure and the South Shore Estuary Reserve 

Office worked with local and regional stakeholders to develop 

a new Coordinated Water Resources Monitoring Strategy 

(CWRMS) for the Reserve with three complementary components: this written report, the project web page, and an 

interactive mapper.
2 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

• Report: Since 2000, when the last CWRMS was published, numerous research projects and studies have 

identified new effects on the ecological health and 

resilience of the Reserve. Many of the recommendations outlined in the 2000 CWRMS were followed, 

while others were not, and a summary of the data gaps 

and recommendations is presented in appendix 1. 

This updated CWRMS highlights major changes since 

2000 that affect water-resource management in the 

Reserve and the significance of recent developments to 

Reserve waterbodies. The updated CWRMS also offers 

recommendations based on perceived data gaps and 

resource-management concerns that have been raised 

by members of the Project Advisory Committee (PAC) 

and other stakeholders. Lastly, the updated CWRMS 

offers recommendations on the collection of metadata 

and a guide for proper quality assurance and quality 

control (QA/QC) documentation of field and laboratory data.

• Web page: The USGS Coordinated Water Resources 

Monitoring Strategy web page (https://doi.org/10.5066/

F7JQ0Z46) has been established to provide a comprehensive perspective of the monitoring programs 

and relevant studies within the Reserve. (A temporary project website [http://www.sserwaterquality.us] 

was established at the onset of the project [2014] and 

remained active until 2017 to provide project updates, 

an interim mapper, and forum for PAC members to 

provide resources and exchange ideas about the project.) The USGS CWRMS web page directs researchers, stakeholders, and the public to relevant documents 

and monitoring data and allows these resources to be 

sorted by type and constituent. The CWRMS report 

and the tables and references associated with the report 

can be downloaded. Additional resources, such as 

links to reports and information about the Reserve, are 

provided through a link to the NYSDOS South Shore 

Estuary Reserve website (NYSDOS, 2017). The USGS 

CWRMS web page also links to the interactive mapper 

developed for the CWRMS.

• Mapper: The interactive mapper (https://ny.water.usgs.

gov/maps/sser/) aggregates available study information from government agencies, academic institutions, 

stakeholders, and citizen scientists and provides links 

(or contact information) for users to obtain available 

data. This information is provided in the context of an 

organization’s monitoring network and the associated 

water-quality constituents or ecological data collected. 

Each of the features can be queried to obtain more 

information about the site, and all information can be 

exported (downloaded). The information provided can 

be filtered on the basis of water-quality constituent 

being collected or analyzed at the site, the datacollection organization, whether data are publicly 

available or not, and other search parameters. Other 

features include the watershed boundaries using 

12-digit hydrologic unit codes (HUC12), the National 

Oceanic and Atmospheric Administration bathymetry 

layer of most bays of the Reserve, a list of New York 

State Department of Environmental Conservation 

(NYSDEC) impaired waters, and NYSDEC shellfish areas.

Though some coordination exists, organizations differ 

in how they are collecting, recording, and archiving waterquality and ecological data within the Reserve. To address 

this, a Project Advisory Committee was assembled in 2015 

to help guide the creation of this CWRMS, which provides 

updates on programs and recommendations on activities 

within the Reserve to address its poor (defined in this report 

as not meeting established criteria or standards for a given 

resource) water quality and ecological health. This CWRMS 

provides a stakeholder-defined list of physical, chemical, and 

biological constituents (table 1) that are either currently being 

measured (2017) or are recommended to be measured at select 

locations throughout the Reserve to assess overall ecological 

health of the contributing systems (surface water, groundwater, land and air resources). This list is based on regulations 

and infrastructure improvements. Many of the constituents 

are being collected to address management issues, and the list 

is for improving efficiencies in the data collection effort. The 

goal is for organizations collecting these data to be coordinated around the same objectives with data delivered through 

a readily accessible public platform.

State of the South Shore Estuary Reserve

The Reserve is a 173-square-mile network of bays and 

tributaries shaped by the south shore of Long Island (New 

York) and the barrier islands that was formed as a result of the 

last ice age (roughly 18,000 years ago). The Reserve receives 

salt water from the Atlantic Ocean through five inlets in the 

barrier islands and freshwater from groundwater and over one 

hundred rivers and streams. Natural and anthropogenic contaminants have been detected in these source waters, as well as 

direct land runoff and atmospheric deposition, and thus have 

been attributed to the decline in estuarine health.

Efforts to improve the water quality of coastal waters 

throughout the State of New York have been ongoing for 

decades. Prioritization of waters identified as impaired by 

pathogens, nutrients, and other factors contributing to eutrophication and closures of areas to shellfishing has allowed the 

NYSDEC to focus resources on areas of greatest need, particularly in the Reserve.

The 2014 NYSDEC list of impaired waters, 303(d), 

identifies 49 waterbodies of the Reserve as being impaired, 

mainly by nutrients, sediment, and pathogens (NYSDEC, 

2014d). See appendix 2 for the list of Reserve waterbodies and impairments. Most waters have been slated for the 

development of either a total maximum daily load (TMDL) 

or a comprehensive assessment since being listed, and seven 

have been completed. Further, nine watersheds or waterbodies 
Introduction 3

Table 1. Constituents collected or proposed for monitoring of water or ecological resources in the South Shore Estuary Reserve, 

New York.

[A constituent may be considered a trophic state indicator (TSI) and (or) a forcing function (FF) on the basis of descriptions provided in the introduction of the 

report. Constituent codes are abbreviations used to cross-reference tables in this report and for the filter function of the website. N, nitrogen; P, phosphorus; PAH, 

polycyclic aromatic hydrocarbon; VOC, volatile organic compound; lidar, light detection and ranging; SAV, submerged aquatic vegetation; TNC, The Nature 

Conservancy; USGS, U.S. Geological Survey; NYSDEC, New York State Department of Environmental Conservation; SoMAS, Stony Brook University School 

of Marine and Atmospheric Sciences; EPA, U.S. Environmental Protection Agency; NOAA, National Oceanic and Atmospheric Administration; Seatuck, Seatuck 

Environmental Association; SPLASH, Operation SPLASH; FWS, U.S. Fish and Wildlife Service; NPS, National Park Service; NWS, National Weather Service; 

NYSDOT, New York State Department of Transportation; --, not applicable]

Constituent Constituent 

code

Trophic state 

indicator tier/

forcing functions

Related biological 

ecological indicators/

sentinels 

(if applicable)

Synergy—organizations with current 

or proposed monitoring

Water

Water temperature WT FF Finfish, shellfish, SAV TNC, USGS, NYSDEC, SoMAS, Suffolk 

County

pH pH -- Shellfish TNC, USGS, NYSDEC

Alkalinity ALK -- Shellfish USGS, Suffolk County, Town of Hempstead, 

SoMAS

Water level (surface water) WL FF Wetlands, grasses USGS, Suffolk County, Town of Hempstead, 

SoMAS

Flow FLOW FF Wetlands, grasses USGS, Suffolk County, Town of Hempstead, 

SoMAS

Groundwater level GWL -- -- USGS, Suffolk County, Nassau County

Depth to bottom (surface water) DEPTH -- -- USGS, Suffolk County, Town of Hempstead, 

NYSDEC, TNC, SoMAS

Salinity/conductivity SAL -- Finfish, shellfish USGS, Suffolk County, Town of Hempstead, 

SoMAS

Chlorophyll a CHL TSI primary Finfish, shellfish USGS, Suffolk County, Town of Hempstead, 

SoMAS

Turbidity TURB -- Finfish, shellfish, SAV USGS, Suffolk County, Town of Hempstead, 

SoMAS

Photosynthetically active radiation/light penetrationPAR FF Finfish, shellfish, SAV SoMAS, Suffolk County

Clarity/Secchi depth CLAR -- Finfish, shellfish, SAV USGS, Suffolk County, Town of Hempstead, 

SoMAS, NYSDEC

Dissolved oxygen DO TSI secondary Finfish, shellfish, SAV USGS, Suffolk County, Town of Hempstead, 

SoMAS

Suspended sediments SS -- Wetlands --

Nutrients (N and P; general) NUT FF Wetlands, grasses USGS, Suffolk County, Town of Hempstead, 

SoMAS, NYSDEC

Orthophosphate OP -- Wetlands, grasses Suffolk County, Town of Hempstead, 

SoMAS, NYSDEC

Total phosphorus TP -- Wetlands, grasses Suffolk County, Town of Hempstead, 

SoMAS, NYSDEC

Nitrate (and nitrite) NO3 -- Wetlands, grasses USGS, Suffolk County, Town of Hempstead, 

Nassau County, SoMAS, NYSDEC

Ammonia (and ammonium) NH3 -- Wetlands, grasses Suffolk County, Town of Hempstead, Nassau 

County, SoMAS, NYSDEC

Total Kjeldahl nitrogen TKN -- Wetlands, grasses Suffolk County, Town of Hempstead, Nassau 

County, NYSDEC

Fecal indicator bacteria FIB -- Wetlands, grasses Suffolk County, Town of Hempstead

Pathogens PATH FF -- NYSDEC
4 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

Table 1. Constituents collected or proposed for monitoring of water or ecological resources in the South Shore Estuary Reserve, 

New York.—Continued

[A constituent may be considered a trophic state indicator (TSI) and (or) a forcing function (FF) on the basis of descriptions provided in the introduction of the 

report. Constituent codes are abbreviations used to cross-reference tables in this report and for the filter function of the website. N, nitrogen; P, phosphorus; PAH, 

polycyclic aromatic hydrocarbon; VOC, volatile organic compound; lidar, light detection and ranging; SAV, submerged aquatic vegetation; TNC, The Nature 

Conservancy; USGS, U.S. Geological Survey; NYSDEC, New York State Department of Environmental Conservation; SoMAS, Stony Brook University School 

of Marine and Atmospheric Sciences; EPA, U.S. Environmental Protection Agency; NOAA, National Oceanic and Atmospheric Administration; Seatuck, Seatuck 

Environmental Association; SPLASH, Operation SPLASH; FWS, U.S. Fish and Wildlife Service; NPS, National Park Service; NWS, National Weather Service; 

NYSDOT, New York State Department of Transportation; --, not applicable]

Constituent Constituent 

code

Trophic state 

indicator tier/

forcing functions

Related biological 

ecological indicators/

sentinels 

(if applicable)

Synergy—organizations with current 

or proposed monitoring

Water—Continued

Total organic carbon TOC -- Wetlands, grasses Suffolk County, Town of Hempstead, SoMAS

Total organic nitrogen TON -- Wetlands, grasses Suffolk County, Town of Hempstead, SoMAS

Major ions ION -- -- --

Fluorescent dissolved organic 

matter

fDOM -- Wetlands --

Oxidation-reduction potential ORP -- -- Shinnecock Tribal Nation

Contaminants of emerging concern 

(pharmaceuticals, personal care 

and domestic-use products, and 

hormones)

CEC -- Finfish, shellfish USGS, SoMAS

Primary pollutants (such as PAHs, 

VOCs, metals, pesticides)

PPOL -- Finfish, shellfish USGS, NYSDEC, EPA, NOAA

Perchlorate ClO4 -- -- USGS, Nassau County

Microplastics MP -- Finfish, shellfish --

Radionuclides RADIO -- Finfish, shellfish SoMAS

Isotope analyses ISOT -- -- USGS, SoMAS

Ecology

Nuisance algae (including harmful 

algal blooms)

NA/HAB TSI secondary, FF Finfish, shellfish SoMAS, Suffolk County

Algal toxins (chemical) ATOX FF Finfish, shellfish SoMAS

Macroalgae MA TSI primary Finfish, shellfish TNC, Town of Hempstead

Subaquatic vegetation SAV TSI secondary -- TNC

Vegetation survey VEG -- -- TNC, Town of Brookhaven, NYSDEC, 

Seatuck

Bed sediment quality BS -- Finfish, shellfish SoMAS

Litter LITTER -- Finfish, shellfish, 

wetlands

SPLASH, EPA

Plankton inventory PLANK -- -- SoMAS

Nekton inventory NEKT -- -- --

Shellfish survey SHELLS -- -- NYSDEC, towns

Shellfish tissue SHELLT -- -- NOAA

Horseshoe crab survey and health HSC -- -- Universities

Invasive flora INVFL -- -- FWS, NPS, TNC, towns, Shinnecock Tribal 

Nation, Audubon Society

Invasive fuana INVFU -- -- FWS, NPS, towns

Macroinvertibrate survey MACRO -- -- NYSDEC

Wildlife survey WILD FF -- FWS, NPS, NYSDEC, Audubon Society
Introduction 5

Table 1. Constituents collected or proposed for monitoring of water or ecological resources in the South Shore Estuary Reserve, 

New York.—Continued

[A constituent may be considered a trophic state indicator (TSI) and (or) a forcing function (FF) on the basis of descriptions provided in the introduction of the 

report. Constituent codes are abbreviations used to cross-reference tables in this report and for the filter function of the website. N, nitrogen; P, phosphorus; PAH, 

polycyclic aromatic hydrocarbon; VOC, volatile organic compound; lidar, light detection and ranging; SAV, submerged aquatic vegetation; TNC, The Nature 

Conservancy; USGS, U.S. Geological Survey; NYSDEC, New York State Department of Environmental Conservation; SoMAS, Stony Brook University School 

of Marine and Atmospheric Sciences; EPA, U.S. Environmental Protection Agency; NOAA, National Oceanic and Atmospheric Administration; Seatuck, Seatuck 

Environmental Association; SPLASH, Operation SPLASH; FWS, U.S. Fish and Wildlife Service; NPS, National Park Service; NWS, National Weather Service; 

NYSDOT, New York State Department of Transportation; --, not applicable]

Constituent Constituent 

code

Trophic state 

indicator tier/

forcing functions

Related biological 

ecological indicators/

sentinels 

(if applicable)

Synergy—organizations with current 

or proposed monitoring

Estuary

Surface elevation table SET -- -- NPS, USGS, FWS

Bathymetry BATHY -- -- NOAA, SoMAS

Edge of wetlands (remote sensing/

drone)

WETLAND -- -- Town of Hempstead

Particle size (bed sediment) PART FF -- SoMAS, USGS

Sediment redistribution SR FF -- SoMAS

Wave energy WVE -- -- --

Wave height WVH -- -- USGS

Air

Precipitation PRECIP -- -- USGS, Town of Hempstead, SoMAS, NWS

Air temperature AT -- -- USGS, Town of Hempstead, SoMAS, NWS

Air quality AQ -- -- NWS

Weather (such as wind, sky, 

humidity)

WEATHER -- -- SoMAS

Infrastructure

Land use LU FF -- Suffolk County, Nassau County

Impervious cover IMPCOV -- -- --

Storm drain outfalls SDO -- -- Towns, NYSDOT, counties

Sewage treatment plant sewerline 

and outfalls

STP FF -- Counties

Topography (aerial, lidar) TOPO -- -- NOAA, USGS

Inundation INUN -- -- USGS, FEMA, EPA

Photography PHOTO -- -- USGS, FWS, NPS, NOAA, SoMAS
6 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

have had a comprehensive management plan created to assess 

in detail the contributions to poor water quality within the 

watershed (table 2; appendix 3). In particular, waterbodies in 

the Reserve requiring the development of a TMDL for nitrogen include Hog Island Channel, Hempstead Lake, Hempstead 

Bay, Moriches Bay, Reynolds Channel, and Great South Bay. 

Furthermore, nitrogen-loading data necessary for groundwater 

flow, runoff, and atmospheric deposition models are not currently available on the scale needed for evaluating the entire 

Reserve. Additionally, recent studies from other parts of the 

country have implicated excessive nitrogen as contributing to 

the increased vulnerability of the salt marshes (vegetation and 

mass) of the region (New York State Department of Environmental Conservation, 2014b). Additional impairments to the 

ecology of the bays and tributaries include excess concentrations of pathogens (from wildlife excrement, leaky sewer 

lines, illicit discharges to storm sewers, and surface runoff) 

and of suspended sediment (suspended; from runoff), and 

aquatic toxicity (caused by low dissolved oxygen or harmful algae and bacteria). Although certain constituents can be 

measured in situ to directly or indirectly inform the extent of 

these impairments throughout the Reserve and provide the 

data necessary to understand cyclic (for example, diurnal with 

tidal exchange) and episodic (for example, during a precipitation event) changes, the number of sites are limited and the 

network of continuous monitoring could be enhanced with 

additional locations to improve spatial resolution and understand localized issues.

The rapid decline in shellfish populations in the early 

1970s, a result of overharvesting, has contributed to declines 

in water quality (including harmful algal blooms) that hinder 

efforts to repopulate the bays with shellfish (Board of Trustees 

of the Town of Southampton, 2001; Town of Brookhaven, 

2013). Efforts by the NYSDEC, The Nature Conservancy 

(TNC), the Shinnecock Tribal Nation, and the Towns of Islip, 

Hempstead, and Babylon, along with other organizations, are 

underway in controlled areas to restore oyster and clam populations throughout the Reserve. Furthermore, recent (2017) 

initiatives by the New York State (NYS) Governor’s Office are 

providing funds and coordination to create shellfish sanctuary 

areas in Bellport Bay, Shinnecock Bay, Hempstead Bay, and 

South Oyster Bay to help improve water quality and bolster 

the economy (New York State Governor’s Office, 2017). 

The goal of continued restoration efforts of natural vegetation along the shoreline, riparian zones, and bay bottom is to 

improve habitat for finfish and shellfish in the bays and enable 

their populations to thrive. The Alosa pseudoharengus (alewife), Mercenaria mercenaria (hard-shell clam), Mytilus edulis (blue mussel), Anguilla rostrata (American eel), and Limulus polyphemus (horseshoe crab) populations that are being 

monitored by State, academic, and nonprofit organizations 

can be used as bioindicators to assess improvements to water 

quality in the bays and tributaries (The Nature Conservancy, 

2012). However, the health of these species is still affected by 

urbanization and physical barriers in spawning areas.

In 2007, the National Oceanic and Atmospheric Administration (NOAA) reported on the level of eutrophication in 

every estuary in the contiguous United States (Bricker and 

others, 2007). The South Shore Estuary Reserve (reported in 

entirety as “Great South Bay”) was characterized by using 

the Assessment of Estuarine Trophic Status (ASSETS) rating 

system, which considers available data for dissolved oxygen, 

chlorophyll a, nutrient loading, algae (macroalgae and harmful 

or nuisance algae), aquatic vegetation, and water clarity to 

determine the overall eutrophication level within four distinct 

zones of the estuary (fresh, fresh tidal, mixed, and seawater). 

The overall eutrophication condition of the Reserve was rated 

at “moderate high” on the basis of data for chlorophyll a, dissolved oxygen, and nuisance algae—data on nutrient loading 

and subaquatic vegetation were not available for inclusion in 

the assessment.

Hurricane Sandy (October, 2012) sparked initiatives to 

review management plans, build resilient infrastructure, and 

revitalize wetlands on Long Island, particularly within the 

Reserve. The Governor’s Office of Storm Recovery (GOSR) 

was created and charged with assessing human and ecological effects of the storm and how to best rebuild. To meet the 

objectives of understanding the effects of the storm, the New 

York Rising Community Reconstruction Program was established by GOSR—there are currently 41 New York Rising 

projects in the Reserve, including locations in the Village of 

Island Park, Valley Stream, Oceanside, and Babylon (GOSR, 

2017). Following the storm, water quality in Hempstead Bay, 

specifically Reynolds Channel, was particularly poor because 

of the discharge of partially treated sewage from the Bay 

Park Sewage Treatment Plant (Kenward and others, 2013). 

As communities began to rebuild, Federal and local agencies, academics, and consulting firms collected data to help 

determine what changes occurred to water and sediment quality of the Reserve (Fischer and others, 2015; NOAA, 2012). 

The long-term effects of these discharges on the wetlands and 

bottom environment of the bays are unknown. However, the 

studies quantified chemical contaminants and modeled transport throughout the bays, and these data provide a reference 

point for future events and for efforts to reshape the sediment (dredging) and rebuild shoreline (improved infrastructure). Changes to the Reserve ecosystem are also addressed 

by modeling of sediment transport along the barrier islands 

(USGS, 2017a) and extensive studies of physical implications 

(tide changes, sediment movement) and chemical implications 

(water quality, flushing) of the breach remaining open at Old 

Inlet (Fire Island National Seashore) (Aretxabaleta and others, 

2014; Flagg and others, 2013; multiple reports listed in Flagg 

and others, 2016).

Current (2017) Management Topics

Managing the resources of the Reserve is a shared 

responsibility. The bays and tributaries of the Reserve afford 

opportunities for commercial and recreational fishing and 
Introduction 7

Table 2. Management plans for water or ecological resources in the South Shore Estuary Reserve, New York.

[Table 2 is a summary of management plans and other documents that present recommendations based on specific locations or resources; an expanded list of 

documents (including updates) is presented in appendix 3]

Document Year 

published Waterway(s) addressed

South Shore Estuary Reserve Comprehensive Management Plan 2001 Entire reserve

Southampton Marine Resources Protection and Management Plan 2001 Shinnecock Bay, Moriches Bay

Potential Impacts of Small-Scale Commercial Mariculture in Southampton Public Waters2003 Shinnecock Bay, Moriches Bay

Green’s Creek and Brown’s River Watershed Management Plan 2006 Green Creek, Brown Creek

Swan River Watershed Management Plan 2007 Swan River

Beaver Dam Creek Watershed Management Plan 2009 Beaverdam Creek

Assessment of Natural Resource Conditions—Fire Island National 

Seashore

2009 Great South Bay, Atlantic Ocean

Massapequa Creek Watershed Management and Corridor Restoration 

Plan

2009 Massapequa Creek

Final Report of the New York State Seagrass Task Force 2009 Entire reserve

South Oyster Bay Hard Clam Population Survey 2009 South Oyster Bay

Town of Oyster Bay South Shore Estuary Reserve Workplan Implementation—Open Space Preservation Plan2010 South Oyster Bay, Massapequa Creek

Natural Resource Program 2010 Entire reserve

Responding to Climate Change in New York State (ClimAID) 2011 Entire reserve

Great Cove Watershed Management Plan 2012 Champlin Creek, Orowoc Creek, Cascade Lakes, 

Penataquit Creek, Awixa Creek, Trues Creek, Lawrence Creek, Thompsons Creek, Watchogue Creek

Forge River Watershed Management Plan 2012 Forge River, Moriches Bay

Great South Bay Ecosystem-Based Management Plan 2012 Great South Bay

Carmans River Conservation and Management Plan 2013 Carmans River

Long Beach NY Rising Community Reconstruction Plan 2014 Hempstead Bay

Climate Risk Report for Suffolk and Nassau 2014 Entire reserve

Suffolk County Comprehensive Master Plan 2035 2015 Entire reserve

Coastal Resiliency and Water Quality in Nassau and Suffolk Counties 2015 Entire reserve

Suffolk County Comprehensive Water Resources Management Plan 2015 All Suffolk County waters in reserve

Suffolk County Subwatersheds Wastewater Plan In progress1 Entire reserve

Harmful Algal Bloom Action Plan In progress1 Entire reserve

Long Island Nitrogen Action Plan In progress1 Entire reserve

Shinnecock Tribal Lands and Bay Resources Management Plan In progress1 Shinnecock Bay, Heady Creek

1

In progress as of May 2017.
8 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

public use (such as swimming), all of which are affected 

negatively by poor water quality. The following subsections 

summarize management topics related to water quality and 

environmental health within the Reserve. Issues identified by 

the PAC and stakeholders have been compiled from meeting 

minutes and are listed in table 3. These issues are addressed in 

subsequent sections of this report, where stakeholder recommendations for filling data gaps and comments about general 

program development and coordination are presented. 

Eutrophication

Nitrogen and phosphorus loading throughout Long Island 

has recently become the focus of several State and local efforts 

(NYSDEC, 2014b, 2017; Suffolk County Government, 2015) 

and has led to the creation of action and management plans 

aimed at reducing loading from point (sewage treatment plant 

and storm drain outfalls) and nonpoint (stormwater runoff, 

onsite wastewater treatment and disposal, and agriculture) 

sources. Major implications of excess nutrients, in particular 

nitrogen, include loss of critical habitats (aquatic vegetation 

such as eelgrass) and salt marshes, low dissolved oxygen 

and hypoxia, macroalgae blooms, toxic algal blooms, and 

loss or depletion of shellfisheries. A strong correlation has 

been shown to exist between nitrogen loading and population growth, with loading to the bays attributed mainly to 

groundwater affected by failing septic systems and antiquated 

cesspools (collectively, inadequate onsite wastewater treatment systems) and agricultural practices, atmospheric deposition, and effluent from wastewater treatment plants (Kinney 

and Valiela, 2011; Stinnette, 2014).

Groundwater loading of nitrogen to embayments presents 

a challenge to managers seeking to reduce nitrogen concentrations to the bays, especially in inland areas with onsite systems 

where groundwater can take decades to reach a tributary or 

seep through the bay bottom (Suffolk County Government, 

2015). Two recent models show that groundwater contributes 

about 69 percent of the nitrogen load to Great South Bay 

(Kinney and Valiela, 2011) and 61 percent of the loads to 

Moriches and Shinnecock Bays (Stinnette, 2014). To provide 

a nitrogen budget for the Reserve, these modeled estimates 

need to be corroborated with historical data available from 

current monitoring programs and new studies of atmospheric, 

runoff-specific, and sediment dynamics of bay bottoms and 

the hyporheic zone of streams. An updated model of areas 

contributing to groundwater recharge is being developed by 

the USGS with the NYSDEC under the Long Island Nitrogen 

Action Plan (LINAP) and could provide the foundation for 

the loading models and decision support tools needed to help 

estimate the effects of changes from wastewater infrastructure 

upgrades, low-impact development, and implementation of 

new sanitary regulations. Current water-quality monitoring 

programs that analyze for nutrients are in place in the bays and 

select streams to provide a glimpse at the overall health of the 

estuary. However, to evaluate the benefits of implementing 

new practices, it would be necessary to coordinate existing 

water-quality monitoring programs and incorporate additional 

resources and tools.

Managing Wastewater Infrastructure

Wastewater infrastructure (including sewage treatment 

plants and onsite wastewater-treatment systems) in the lowlying areas of the Reserve spans the population gradient and 

has been tied directly to the water quality of the bays and 

tributaries (Monti and Scorca, 2003). The extent of wastewater 

management systems (that is, centralized sewage treatment 

plants and municipal separate storm sewer systems) within the 

Reserve, in general, correlates well with population density, 

with the western part being sewered and the eastern part 

largely unsewered. Inadequate onsite wastewater treatment 

systems are believed to contribute substantial nitrogen loading 

to the aquifer system (Stinnette, 2014), whereas the effects 

of implanting sewage treatment in higher density areas can 

be observed in historical groundwater and surface-water data 

(Monti and Scorca, 2003). Sewage treatment infrastructure in 

Nassau County and western Suffolk County is monitored as 

part of regulatory requirements (NYSDEC, 2016b). Monitoring to assess the immediate and gradual improvements 

expected from these changes is important to gaging ecosystem 

response to both (1) the shift from inadequate onsite wastewater treatment systems to centralized sewage treatment plants or 

onsite treatment (or the innovative alternative onsite wastewater treatment systems being tested by Suffolk County since 

2015) and (2) upgrades to existing sewage treatment plants. 

In particular, organic and inorganic (organic nitrogen, nitrate, 

nitrite, ammonium) forms of nitrogen and suspended solids in 

waters adjacent to outfalls and in the shallow aquifer would 

exhibit the greatest changes over the short term.

Five major sewage infrastructure projects are proposed in 

Nassau and Suffolk Counties to improve resiliency and water 

quality.

• Reduce extensive nitrogen pollution to the Forge 

River and Great South Bay by constructing new 

sewage infrastructure on municipal property near the 

Brookhaven Calabro Airport.

• Reduce nitrogen and pathogen pollution in the Carlls 

River and Great South Bay by connecting parcels not 

currently sewered to the Bergen Point sewer system 

within the Southwest Sewer District.

• Reduce nitrogen pollution and pathogens in Connetquot River, Nicoll Bay, and Great South Bay by connecting parcels to the Bergen Point sewer system.

• Reduce nitrogen and pathogen pollution in Patchogue 

River and Great South Bay by connecting remaining 

parcels to the Patchogue sewer system within the Village of Patchogue Sewer District.

• Reduce nutrient pollution by expediting upgrades at 

the Bay Park Sewage Treatment Plant and installing a 
Introduction 9

Table 3. Management issues identified by the Project Advisory Committee for the South Shore Estuary Reserve Coordinated Water 

Resources Monitoring Strategy.

[Abbreviations of the related management plan documents reference table 3–1. NYSDOS, New York State Department of State; Reserve, South Shore Estuary 

Reserve; STP, sewage treatment plant; FEMA, Federal Emergency Management Agency; NYSDEC, New York State Department of Environmental Conservation; SCDHS, Suffolk County Department of Health Services]

Management issue from stakeholder input

Management 

issue 

number

Document(s) with topic 

relevant information

Maintaining best management practices is challenging in terms of both funding and time. 

They do not always function as they were designed.

MI1 --

Gathering data from multiple organizations is powerful when used to support public policy. 

It adds authority to data when different groups get the same result.

MI2 --

The NYSDOS has no comprehensive plan or budget for spending in the Reserve. MI3 SSER CWRMS 2000, SSER CMP

There has been limited data sharing between New York State agency offices. MI4

There are currently issues with the data sharing and standardization. Resources are needed to 

help municipalities preserve/organize water quality and ecological health data electronically and make available to the public in a standardized manner.

MI5 --

Connection of Long Beach STP to the Bay Park STP may not happen due to lack of funding. MI6 --

FEMA’s new flood zone maps do not meet the needs of some towns on the south shore. MI7 --

Lack of resources prevents monitoring of finfish. MI8 --

There is lack of long-term funding for monitoring projects. MI9 --

NYSDEC needs better water-quality data to correlate with water-quality standards and better understand how water quality is affecting the collapse of the ecological system in the 

Reserve.

MI10 --

Inquiries into Administration for Native Americans funding were recommended for monitoring and resiliency work within Shinnecock Tribal lands.MI11 --

Heady Creek storm drain is a potentially significant source of contaminants to the 

Shinnecock Bay. Oysters can be raised on the east side of Shinnecock Bay but must be 

transported to the west side to be edible.

MI12 SHIN RMP

Chemicals used for the treatment of marine wood used for bulkheads are leaching into the 

bays.

MI13 --

There is concern about the deteriorating water quality in the western portions of the 

Shinnecock Bay reaching Shinnecock Tribal lands because the Tribe plans to reinstate the 

hatchery on the southeast side of the peninsula. Degradation in Shinnecock Bay tributaries and bays has been observed west of Ponquogue Bridge. Work on this issue is being 

addressed by SCDHS.

MI14 SHIN RMP, SH MRPMP, SH 

SFS, SHIN RMP

Interpretation of sediment analysis in the western portion of Hempstead Bay is difficult 

because of dredging.

MI15 --

It is difficult making sense of data from Hurricane Sandy sediment sampling. Samples 

should have been collected along the coast where mud is present.

MI16 --

Mill River (Hempstead) sediment near auxiliary outfall has very high levels of microplastics.MI17 --

Poor water quality and low dissolved oxygen has been observed in embayments at night. MI18 GSB EMP, SC CWRMP, LINAP, 

HAB AP, NRA FIIS

Wetlands are being lost at an alarming rate. In Middle Bay (Hempstead), three-quarters of 

marsh islands have disappeared over past 50 years.

MI19 SSER CWRMS 2000

Several ponds in Nassau County parks are clogging, and after deepening have issues. MI20 --

Shellfish closures throughout the Reserve continues to be a economic issue. MI21 GSB EMP

Killifish and forage fish are lacking—the reason for this is not apparent. MI22 --

Adult clams are threatened in Great South Bay due to brown tide and poor bottom conditions, which compromise spawning and reproduction ability.MI23 SC CWRMP, SC CMP 2035, 

CRWQ, LINAP, HAB AP
10 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

Table 3. Management issues identified by the Project Advisory Committee for the South Shore Estuary Reserve Coordinated Water 

Resources Monitoring Strategy.—Continued

[Abbreviations of the related management plan documents reference table 3–1. NYSDOS, New York State Department of State; Reserve, South Shore Estuary 

Reserve; STP, sewage treatment plant; FEMA, Federal Emergency Management Agency; NYSDEC, New York State Department of Environmental Conservation; SCDHS, Suffolk County Department of Health Services]

Management issue from stakeholder input

Management 

issue 

number

Document(s) with topic 

relevant information

Oyster Bay is in good position to understand differences in shellfish survival and breeding 

by comparing Hempstead Bay and Great South Bay.

MI24 --

There are concerns over flooding about higher groundwater levels (2 feet) along the South 

Shore in the future.

MI25 --

Groundwater contamination is a major contributor to declining water quality of the bays. 

For example, Tiana Bay affected by MTBE (methyl tert-butyl ether) laden groundwater 

from gas stations.

MI26 GSB EMP, SC CWRMP, LINAP, 

HAB AP

With warmer temperatures, more pathogens have been observed in water/beaches resulting 

in beach closures.

MI27 --

Invasive Phragmites are abundant throughout the Reserve. MI28 SHIN RMP

Advanced wastewater treatment options (onsite denitrifying and centralization) are being 

investigated in Suffolk County and on Shinnecock Tribal lands.

MI29 SHIN RMP

Onsite wastewater disposal systems in areas with shallow depth to water have failed/flooded 

and backed up to the surface.

MI30 --

There is concern over horseshoe crab harvesting and population sustainability. MI31 NRA FIIS, GSB EMP

Canada geese can contribute to high pathogen levels in tributaries, bays, and ponds throughout the Reserve.MI32 --

Watercraft such as boats and jet skis are causing harm to grasses in shallow waters. MI33 GSB EMP

The increasing number of storms is damaging marshes and submerged aquatic vegetation. MI34 --

There has been an increase in the abundance of Ruppia maritima (widgeongrass), a type of 

submerged aquatic vegetation.

MI35 --

Fish kills in the Reserve are a concern and are caused by low dissolved oxygen, and also 

affected by temperature and atmospheric nitrogen. Real-time water quality data do not 

always exist in impacted waters.

MI36 --

Natural oyster restoration efforts have been unsuccessful due to disease, but oyster aquaculture has had success.MI37 SSER CWRMS 2000, SSER 

CMP, GSB EMP, SOB HCPS

As development continues within the Reserve, the burden of nutrients and other contaminants to the bays and groundwater.MI38 --
Introduction 11

midstage nitrogen treatment system to improve water 

quality in the Hempstead Bay and protect extensive 

marsh islands, which serve as natural flood protection 

barriers for southern Nassau County (GOSR, 2014). 

Further reduction of nutrient loading to the Reserve is 

expected following the diversion of effluent from Bay 

Park Sewage Treatment Plant to Cedar Creek Water 

Pollution Control Plant (which discharges to the Atlantic Ocean) and the proposed conversion of Long Beach 

Sewage Treatment Plant to a pump station to transport 

wastewater to the Bay Park Sewage Treatment Plant.

The current water-quality monitoring program conducted 

by the Town of Hempstead and Nassau County serves as a 

baseline for changes in nutrient loading and how the western 

bays of the Reserve respond over time. There is some debate 

as to how altering the loading of nutrients to the system would 

affect the current ecological balance (John Tanacredi, Molloy College, written commun., 2016). Poor water quality in 

Hewlett and Brosewere Bays has been attributed, in part, to 

poor circulation and flushing (Swanson and others, 2013) and 

the Bay Park Sewage Treatment Plant and linked to increased 

Ulva growth throughout Hempstead Bay over the past decade. 

Some researchers suggest, however, that a sharp decrease in 

nitrogen to the bays could lead to marsh island loss—an issue 

exacerbated by motorboat traffic and continuous erosion by 

natural wind-driven waves (James Browne, Town of Hempstead Conservation and Waterways, oral commun., 2015).

Municipal separate storm sewer system (MS4) regulation requires towns to monitor the stormwater infrastructure 

to prevent contaminant discharge according to an approved 

stormwater management program. Water quality (constituents 

include suspended sediment, conductivity, nutrients, primary 

pollutants), discharge, and flow (of receiving waterbody) data 

are needed to make informed decisions about meeting management objectives and permit requirements, as well as to provide data for model input (NYSDEC, 2008). A 2009 American 

Recovery and Reinvestment Act grant was awarded by the 

NYSDEC to support stormwater management planning in over 

100 communities in Nassau and Suffolk Counties, particularly 

in MS4-permitted systems that discharge to waters impaired 

by pathogens (NYSDEC, 2012).

Pathogens

Bacteria and viruses associated with sewage and wildlife 

excrement continue to affect public beaches and shellfishing in the Reserve. Indicator bacteria are used to determine 

whether waters are safe for recreation or fishing. Agencies 

responsible for sampling waters of the Reserve for indicator 

bacteria include the NYSDEC, the health departments of Nassau and Suffolk Counties, the National Park Service (NPS), 

and New York State Office of Parks, Recreation, and Historic 

Preservation. Total and fecal coliforms are used for determining closures of areas to shellfishing. Per U.S. Environmental 

Protection Agency (EPA) guidelines and recommendations 

made in the 2000 CWRMS, Enterococcus spp. (enterococci) 

are being used as a fecal indicator at marine bathing beaches 

because enterococci correlated better with the incidence of 

illness than coliforms (Boehm and Sassoubre, 2014). Elevated 

indicator bacteria concentrations at beaches and in shellfish 

areas following heavy precipitation continue to result in closures based on current data and predictions based on historical 

data. Automated public alerts, such as USGS Nowcast (Francy 

and others, 2013; USGS, 2016a), have been developed in other 

areas. These alert systems rely on real-time weather data and 

current and historical bacteria data collected by local health 

agencies. The data are ingested by the EPA Virtual Beach 

program (EPA, 2017b), and the resulting models are designed 

to forecast closures because of high pathogen concentrations. 

This model performs well as long as an active and rigorous 

water-quality sampling program is in place.

Techniques for identifying sources of pathogens (for 

example, stormwater runoff, direct loading from wildlife, and 

the influence of inadequate onsite wastewater treatment), such 

as microbial source tracking, help inform load-reduction initiatives and TMDL regulation. Advanced methods that use DNA 

and RNA sequencing could potentially differentiate contributing species and types of bacteria that are pathogenic (Griffin 

and others, 2000; Corsi and others, 2016). With these methods 

and with data on the appropriate water-quality constituents 

(nutrients, metals, natural and anthropogenic organic compounds), resource managers can work towards implementing 

infrastructure upgrades and wildlife controls and updating 

regulations on effluent and discharges.

Total Maximum Daily Loads

A TMDL for impaired waterbodies provides resource 

managers with a planning tool and potential starting point for 

restoration or protection activities with the ultimate goal of 

attaining or maintaining water-quality standards (EPA, 2017a). 

Developing a TMDL for nitrogen, phosphorus, pathogens, 

or other constituents requires a considerable investment of 

funds and personnel to compile existing data and collect any 

additional data needed to model and enforce recommended 

changes in the loading. Leveraging and standardizing existing 

data collection efforts to generate data necessary for a TMDL, 

including source assessment and fate and transport studies, 

could help offset costs. Other environmental and human factors necessary to assess when developing a TMDL include 

land-use designation and sewerage, precipitation, and hydrologic properties of the groundwater and surface waters.

The sources and concentrations of contaminants to 

some of the waterbodies of the Reserve have been modeled 

or estimated for nitrogen, and implementing a strategy (even 

without a TMDL) for the reduction of total loading to the 

bays throughout Long Island is the goal of the Long Island 

Nitrogen Action Plan initiated by the NYSDEC in cooperation 

with Nassau and Suffolk Counties. In the western bays of the 

Reserve, researchers at the Stony Brook University School of 

Marine and Atmospheric Sciences (SoMAS) are working with 
12 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

the NYSDEC and the New York State Department of State to 

compile a dataset to develop a TMDL for nitrogen (including 

data collected by the Town of Hempstead, Nassau County, 

USGS, and SoMAS). The Nitrogen Load Model used for 

Great South Bay (Kinney and Valiela, 2011) and the eastern 

bays of the Reserve (Stinnette, 2014) would also allow for 

comparison to the other parts of the Reserve already assessed. 

Monitoring within subwatersheds would support and validate 

the model and refine data inputs for nitrogen, phosphorus, 

pathogens, sediment, and other contaminants identified on the 

NYSDEC 303(d) list (Lloyd, 2014).

Harmful Algal Blooms

Harmful algal blooms (HABs) were included as a reason 

for impairment on the NYSDEC 303(d) list for Great South 

Bay, Moriches Bay, Quantuck Bay, and Shinnecock Bay 

starting in 2010. Since the CWRMS was drafted in 2000, 

the Reserve has experienced an increase in the frequency 

of Aureococcus anophagefferens (brown tide), which first 

appeared on Long Island in 1985, in the Great South Bay and 

eastern bays of the Reserve (Suffolk County Government, 

2016). Identification of Alexandrium fundyense (red tide) and 

Cochlodinium polykrikoides (rust tide) also occurred for the 

first time in 2002 and 2004, respectively, and has recurred in 

subsequent years (Branca and Focazio, 2009). Though blooms 

of algae associated with brown, red, or rust tides can harm 

shellfish, toxins produced by red tide are toxic to finfish and 

those from rust tide are toxic to humans.

The issue of harmful algal blooms is international as they 

affect fresh and marine waters and lead to closures of shellfisheries, with economic implications for fishermen, tourism, 

and recreation, as well as harming wildlife. Efforts are underway to understand the causes and factors driving these blooms 

in the Reserve and throughout the world. Factors currently 

shown to influence the proliferation of HABs in estuaries 

include nitrogen and phosphorus loading (from groundwater 

affected by inadequate onsite wastewater treatment systems, 

atmospheric deposition, and stormwater runoff), poor circulation, and micronutrient concentrations (Paerl, 1997; Heisler 

and others, 2008; Gobler and others, 2012; HattenrathLehmann and others, 2015). The improvements to water quality and decline in brown tide observed in the eastern Great 

South Bay have been attributed to the opening of Old Inlet 

breach on Fire Island following landfall of Hurricane Sandy. 

The type of toxins produced by each HAB and the extent to 

which a bloom occurs are also being studied from samples 

collected in the Reserve and elsewhere on Long Island (Gobler 

and others, 2012).

Experts from around the region assembled for the Long 

Island HAB working group (led by New York Sea Grant and 

Suffolk County Department of Health Services [SCDHS]) to 

create the Suffolk County Harmful Algae Bloom Action Plan 

(Wise, 2017) for the Reserve, Peconic Estuary, Long Island 

Sound, and inland fresh waterbodies of Long Island. It takes a 

coordinated, multidisciplinary monitoring and research effort 

to address the HABs issue. One example of Federal, State, and 

local agencies together addressing the HABs problem in their 

community is in Tampa Bay, Florida. Starting around 1970, 

the population of the Tampa Bay watershed increased to the 

point where the human effect on the Bay led to major waterquality impairments. Through a concerted effort and continued 

monitoring and response (that is, infrastructure improvements, 

runoff controls, and community outreach), the community 

rehabilitated the waters in the Tampa Bay watershed (Tampa 

Bay Estuary Program, 2013). An extensive water-quality monitoring program is still in place to ensure continued improvement and compliance with regulation throughout the bay area.

Wetland Loss

Resource and emergency managers are increasingly 

recognizing the importance of wetlands (such as shoreline and 

island marshes) in mitigating infrastructure damage and shoreline erosion from extreme weather events in the wake of Hurricane Sandy (Wagner and others, 2014). Marshes in particular 

provide a buffer to storm surges and wave attenuation (Möller 

and others, 2014; Stark and others, 2015). The Wetlands Stewardship Strategy introduced by Suffolk County is expected to 

provide the basis for increased Federal and State aid, which 

will allow the county to rehabilitate more than 2,500 acres of 

damaged wetlands, thereby restoring habitat and improving 

shoreline resiliency (Leuzzi, 2015). Other marsh restoration 

projects funded by National Fish and Wildlife Foundation 

grants are underway throughout the Reserve to assist Suffolk 

and Nassau Counties, Cornell Cooperative Extension, the 

Shinnecock Tribe, the towns and villages, other government 

and nonprofit organizations, and academia to engineer and 

rebuild shorelines to serve as habitat and natural buffer against 

wave energy.

The NYSDEC (New York State Department of Environmental Conservation, 2014; Cameron Engineering & Associates, LLP., 2015), the Town of Hempstead Department of Conservation and Waterways, and the Suffolk County Department 

of Public Works actively monitor changes in wetland loss 

by using aerial imagery and geographic information systems 

(GISs) to track the progress of efforts to restore marshes along 

the shore and in the bays. Recognized influences on wetlands 

include nutrient loading, boat traffic, and shoreline changes 

(such as bulkheading). In coastal areas, high nitrogen loading has been implicated as a driver in marsh loss (Deegan and 

others, 2007) because the root network of wetland grasses may 

grow shallow and thus would not be able to anchor and protect 

the sediment from erosion. This may mean that efforts to 

construct wetlands and improve resiliency could be negatively 

influenced by the continuous nutrient loading to the bays of 

the Reserve from groundwater seepage and other contributors 

of nitrogen. Other drivers of wetland loss include sea-level rise 

and increased wave energy from watercraft wakes. Therefore, 

in monitoring wetland loss, it is important to continue assessing water quality, develop loading estimates, and study vegetation density and shoot-to-root ratios in and around wetlands 
Introduction 13

as restoration efforts (and infrastructure changes that alter 

nitrogen loadings) are implemented.

Decline in Fisheries

Shellfish populations in the Reserve continue to decline, 

though efforts to revitalize populations through hatcheries, 

selective farming, and habitat restoration (The Nature Conservancy, 2012) are ongoing. Improved water quality is expected 

if filtering bivalves become more abundant, but improved 

water quality is also needed to ensure successful restoration. 

Currently, monitoring data are collected near the surface 

by Suffolk County in Great South Bay and by the Town of 

Hempstead in Hempstead Bay, and monitoring of bottom 

temperature, pH, and dissolved oxygen is generally limited to 

shellfish areas.

Poor water quality has been implicated in the recent fish 

kills in the Peconic Estuary and Long Island Sound. There is 

concern that the Reserve will experience fish kills on a larger 

scale if water quality is not improved. Further complicating the issue is the way in which some fish species (such as 

Brevoortia tyrannus [menhaden]) move and feed, which can 

result in a large number being present in waters with insufficient flow or mixing to sustain dissolved oxygen concentrations necessary for survival. During the large fish kill in the 

Peconic Estuary, near the mouth of the Peconic River in spring 

2015, the USGS Peconic River at County Road 105 waterquality monitoring station (station 01304562) reported a dissolved oxygen concentration decrease to near zero. However, 

at the same time, chlorophyll concentrations were elevated, 

which indicated high algae concentrations. These data raised 

the question of whether the fish suffocated or were poisoned 

by HABs. Therefore continuous data, along with toxicological 

studies, are necessary to better understand the causes of, and 

how to limit, major fish kills.

Aquatic Vegetation Restoration

Loss of nearshore (for example, Spartina) and submerged 

vegetation (for example, eelgrass) has resulted from the 

decline of water quality and the introduction of invasive species to the Reserve, particularly in the eastern bays (NYSDEC, 

2004; New York State Seagrass Taskforce, 2009). Submerged 

aquatic vegetation (SAV) provide critical habitat for finfish 

and shellfish to feed, reproduce, and avoid predation while 

increasing dissolved oxygen concentrations in bottom waters. 

A Reserve-wide survey of seagrass in 2002 showed eelgrass 

had declined considerably; the decline was attributed in part 

to poor water clarity that prevented sunlight from reaching the 

bottom (New York State Seagrass Taskforce, 2009). Subsequent surveys by SoMAS and Cornell Cooperative Extension 

in the Great South Bay and eastern bays of the Reserve have 

also been conducted on a local scale. Water-quality constituents critical to revitalizing submerged vegetation include light 

penetration (turbidity), bottom water temperature, and pH.

Climate Change and Resiliency

In 2007, the New York State Legislature created the Sea 

Level Rise Task Force and charged it with preparing a report 

that addresses issues related to climate change, sea-level rise, 

and ocean acidification. Led by the NYSDEC, the Task Force 

included a diverse membership of representatives from State 

and local government agencies, nongovernmental organizations, and affected communities. Their work presents recommendations for an action plan to protect coastal communities 

and natural resources from rising sea levels (New York State 

Sea Level Rise Task Force, 2010). The NYSDEC continues 

to evaluate potential effects of climate change through reports 

and updates to ClimAID (NYSDEC, 2014c). Following 

Hurricane Sandy, this effort was renewed and new initiatives 

were proposed. Upgrades to wastewater infrastructure (that 

is, sewer systems and stormwater systems) within the Federal 

Emergency Management Agency (FEMA) category 1 flood 

zones are underway at an accelerated rate with help from 

Federal and State grants. Funds are also being provided to help 

rebuild and harden coastal wetlands to provide a natural barrier for wave attenuation and ecosystem services (New York 

State Sea Level Rise Task Force, 2010).

The Community Risk and Resiliency Act (NYS bill 

A06558/S06617–B) was developed to provide guidance for 

NYS on predicted sea-level rise, storm surge and flooding in 

facility siting, recommendations for permitting and funding, 

State Smart Growth Public Infrastructure Policy Act criteria 

(ENV §6–0107), modeling of local laws concerning climate 

risk, and guidance on natural resiliency measures (NYSDEC, 

2014a). FEMA produced the State Mitigation Plan, effective 

in March 2016, to demonstrate commitment to reducing risks 

from national hazards and serve as a guide for decision makers 

(FEMA, 2015). 

In addition to sea-level rise, climate models predict 

coastal storms that are greater in intensity, similar to Hurricane 

Irene and Hurricane Sandy (and the nor’easters that followed), 

in the future. How to protect communities, critical infrastructure, and ecological habitat is a challenge facing all levels 

of government. In recent years, priority has been placed on 

building resiliency, with a focus on sustainability. The storm 

surge brought by Hurricane Sandy caused widespread damage 

to homes, bulkheads, piers, and wastewater-treatment infrastructure. While tidal wetlands and marsh islands in the bays 

have the capacity to lessen the effect of storm surge, wetland 

loss in the western bays of the Reserve has been documented 

(NYSDEC, n.d.[b]; Cameron Engineering & Associates, 

LLP., 2015). This wetland loss makes homes along the shore 

more susceptible to future damage, particularly in areas now 

included in the Federal Emergency Management Agency’s 

revised flood map (https://msc.fema.gov/portal/).

Among the long-lasting effects of Hurricane Sandy is the 

breach within the boundaries of Fire Island National Seashore 

(NPS, 2017). Old Inlet is within the Otis Pike Fire Island 

High Dune Wilderness. Two other breaches formed in Smith 

Point County Park and east of Moriches Inlet but were closed 
14 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

soon after the storm by the U.S. Army Corps of Engineers 

(USACE). The effects of the breach on ecological, biological, and physical constituents are not completely understood, 

though improved water quality in the Bellport Bay and surrounding waters may allow the ecosystem to recover from 

decades of poor flushing and vegetation loss (Flagg and others, variously dated). The USGS (2016b), NPS, SoMAS, and 

Cornell Cooperative Extension continue to monitor sediment 

transport, velocity of currents, and changes in basic waterquality constituents of the bays and capitalize on the potential 

for restoring eelgrass and shellfish to the area.

Extreme weather events are expected to increase in the 

region during the coming years because of climate change 

(Rosenzweig and others, 2011). Improving resiliency in the 

coastal communities of the Reserve requires assessing the 

ability for ecosystem and infrastructure to respond to changing environmental conditions (including sea-level rise) 

and rebound quickly after a storm. Agencies responsible 

for protecting the coastal communities are recognizing the 

importance of investing in adaptive measures that can reduce 

vulnerability and risk to extreme events (AKRF Inc., 2015; 

GOSR, 2017). Studies and models have been implemented 

to collect hydrologic data to better predict the intensity of the 

next storm on the coastal beaches, wetlands, and communities 

(USGS, 2014; NOAA, 2014). Furthermore, regional studies 

from Cape Cod (Cape Cod Commission, 2013), Chesapeake 

Bay (Lyerly and others, 2014), and Puget Sound (Puget Sound 

Partnership, 2012) emphasize the importance of an ecosystembased monitoring strategy that can identify areas of concern 

and provide input for refining models aimed at assessing 

changes in wastewater infrastructure. Linking infrastructure 

vulnerability to ecological data could also help in assessing the 

risk to habitat and wildlife populations (by maintaining and 

expanding inventories such as the Park Species List created 

by the NPS (2016) when rebuilding or creating coastal buffer 

wetlands (through State and local land-buying programs) to 

protect against a rising sea level.

Critical to supporting models and resiliency efforts is 

the continued monitoring of constituents to gage climate 

change and the sentinel species that are affected. Necessary 

constituents being collected for long-term tracking of climate 

change and sea-level rise are water temperature, salinity, pH, 

water level, and chlorophyll concentrations. Ancillary data 

include nutrient concentrations, precipitation quantities, and 

air temperature data. Sentinel species in the Reserve that 

provide insight into changes in ecosystem health (from climate 

change or otherwise) include mussels and hard-shell clams 

(pH, temp), horseshoe crabs (pH, temp, salinity), eelgrass 

(pH, temp, water level), and wetland and marsh island grasses 

(nutrients, water level, salinity).

Forcing Functions

Much of the research, comments, and discussion presented in chapter 3 of the 2000 CWRMS regarding factors that 

ultimately contribute to the water quality and ecological health 

of the Reserve is still valid today (Ecologic LLC, 2000). The 

forcing functions, defined as “physical, chemical, biological, 

and human-induced factors which play a major role in determining water quality” (Ecologic LLC, 2000), were explained 

in the context of the body of knowledge and model predictions 

available at the time. An update is presented here with new 

information based on recent studies and events.

Many of the physical factors remain the same as in the 

2000 CWRMS; however, the following updates apply:

1. Circulation and water quality have changed around the 

Old Inlet breach—initial data suggests water quality in 

Bellport Bay has improved with the increased flushing 

(Flagg, 2013; Brown, 2013).

2. Major coastal storms caused substantial bed-sediment 

redistribution—scouring and deposition—to an extent 

not quantified (Hydroqual, 2013; Swanson and others, 

2013).

3. Inlets and tributaries of the Reserve have been dredged 

by Suffolk County and USACE to maintain navigation, 

and the dredging has altered circulation and sediment 

transport into and out of the bays and tributaries.

4. Flow models in Hempstead Bay indicate flow restrictions in Hewlett and Brosewere Bays (Swanson and others, 2013; Hydroqual, 2013), which have been attributed 

to poor water and sediment quality (Fischer and others, 

2015).

5. Recent studies of submarine groundwater discharge to 

Great South Bay (from tributaries and across the bay 

floor) using direct-seepage measurements and radioisotopes estimate a groundwater discharge of around 

3.5–4.7 × 109 liters per day (Beck and others, 2007); 

groundwater discharge estimates have not been calculated for Hempstead Bay or the eastern bays of 

the Reserve.

6. Model estimates of groundwater recharge areas are 

available (CDM, 2003; updated in 2009).

7. Mean sea level rose 4.35 millimeters per year over 

15 years at Bergen Point, New York, by 2016 (NOAA, 

2016).

8. Average precipitation in the area is currently 120 centimeters per year, though this value is projected to 

increase because of climate change—precipitation 

rates across New York State could increase by approximately 1–8 percent by 2020, 3–12 percent by 2050, and 

4–15 percent by 2080 (Horton and others, 2014; for 

updates see New York State Energy Research and Development Authority, 2014).

Many of the chemical factors remain the same as in the 

2000 CWRMS; however, the following updates apply:
Introduction 15

1. Dissolved oxygen concentrations in bottom waters of the 

Great South Bay south of Connetquot River have been 

found to be hypoxic beyond typical diurnal cycling in 

some areas by The Nature Conservancy and SoMAS; 

marsh ditches experience anoxic conditions at night.

2. Nitrogen loading—total nitrogen estimates:

A. Great South Bay—total nitrogen: 50 percent wastewater origin, 16 percent atmospheric deposition on 

land (indirect), 26 percent atmospheric deposition 

to the bay (direct), and 7 percent use of fertilizer on 

land (Kinney and Valiela, 2011)

B. Eastern bays—total nitrogen: 65 percent wastewater, 

20 percent fertilizer, and 15 percent atmospheric 

deposition (Stinnette, 2014)

C. Western bays—dissolved nitrogen: 79.4 percent of 

dissolved nitrogen from sewage treatments plants at 

Bay Park and Long Beach (http://www.unitedwaterlongisland.com/about-the-western-bays/)

Many of the biological factors remain the same as in the 2000 

CWRMS; however, the following updates apply:

1. Harmful algal blooms in the Reserve have increased 

in frequency and the species type. (Gobler and others, 

2008; Suffolk County Government, 2016).

A. Aureococcus anophagefferens (brown tide) blooms 

were first documented in the Great South Bay in 

1985 and have since appeared with varying degrees 

of concentration and at varied locations throughout 

the Reserve, with large blooms in 2008 and 2013.

B. Cochlodinium polykrikoides (rust tide) blooms have 

been documented in Shinnecock Bay since 2004.

C. Alexandrium fundyense (red tide) blooms have been 

recorded in Shinnecock Bay in 2002, 2008, 2009, 

and 2012, though closure was only necessary 1 year; 

ingestion of shellfish harvested from bloom waters 

potentially affects human health.

D. Cyanobacteria (also known as blue-green algae) 

affect marine and freshwater environments; nearly 

annual reports of occurrence in Lake Agawam and 

Mill Pond in Southampton.

2. Eelgrass survey estimated coverage—aerial photographs 

taken in 2002 revealed about 20,015 acres of the Reserve 

currently support seagrass, of which 14,744 acres are in 

Great South Bay (New York State Seagrass Task Force, 

2009). Continued updates to SAV surveys are necessary 

for the accurate assessment of seagrass growth patterns 

(that is, losses and gains).

3. Shellfish populations in the Reserve are low despite 

restoration efforts (such as expanding the number of 

hatcheries in the Reserve and closures of areas to shellfishing) and public outreach, which have been underway 

for over a decade with the hopes of restoring pre-1970s 

conditions.

4. Recent management plans are addressing dams and 

other physical structures that prevent fish from moving 

upstream—efforts are underway to remove impediments 

or construct fish ladders on several tributaries (Carmans 

River [Suffolk County Government, 2014] and Massapequa Creek) as a means of restoring the natural ecology within the watershed.

Many of the human-induced factors remain the same as in the 

2000 CWRMS; however, the following updates apply:

1. Total population of the six towns that are included in 

the Reserve (Hempstead, Oyster Bay, Babylon, Islip, 

Brookhaven, Southampton) increased about 3.5 percent 

over the past 15 years. The population was approximately 2.12 million people in 2002, 2.18 million in 

2010, and 2.20 million in 2014. (U.S. Census Bureau, 

2014). The population that lies within the boundaries 

of the Reserve (fig. 1) increased 1.1 percent between 

2000 and 2010 based on block-level U.S. Census data 

(Manson and others, 2017). The percent change has been 

calculated for each town.

A. Hempstead decreased by 1.7 percent.

B. Oyster Bay decreased by 4.2 percent.

C. Babylon increased by 0.6 percent.

D. Islip increased by 2.7 percent.

E. Brookhaven increased by 9.0 percent.

F. Southampton increased by 5.1 percent.

2. In addition to what is listed in the 2000 CWRMS regarding groundwater contributions, the effects of increasing 

pumping to meet demand of an increasing population 

are being evaluated by water purveyors and government 

agencies. Increases in pumping can result in the lateral 

and vertical transport of contaminants introduced at the 

surface (for example, oil spills) or subsurface (for example, cesspool leachate), effectively transporting younger 

water deeper into the aquifers (Misut, 2011; EPA, 2015). 

Greater pump rates near the coast can result in saltwater 

intrusion in the aquifers (Barlow, 2003; USGS, 2016c) 

and potentially reduce the supply of freshwater to 

streams through base flow (Barlow and Leake, 2012).

Trophic State Indicators

Eutrophication of a waterbody is caused, in part, by 

human influences on a watershed. Though natural eutrophication occurs, the degraded water quality of the Reserve is 

mainly a result of the excess nutrient loading and other factors 
16 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy 72°W 73°W 74°W 41°N 40°30'N

L o n g I s l a n d S o u n d

ATLANTIC OCEAN

CONNECTICUT NEW YORK

NEW

JERSEY

Hudson River

SUFFOLK

NASSAU

QUEENS

KINGS

0 10 20 MILES0 10 20 KILOMETERS

EXPLANATION

Figure areasSouth Shore Estuary

Reserve extent

Extent for figure 2

Extent for figure 3

Extent for figure 4

Base from National Oceanic and Atmospheric Administration medium-resolution 1:70,000-scale digital vector shoreline data and U.S. Geological Survey digital data, 2016Projection: State Plane, New York, Long IslandNorth American Datum of 1983

Figure 1. Political boundary of the South Shore Estuary Reserve, Long Island, New York.
Introduction 17

listed in the previous section. Over the past decade, indicators 

have been developed by the National Oceanic and Atmospheric Administration to readily assess the conditions of a 

waterbody by using inputs for primary and secondary indicators (Bricker and others, 2007). The waters are then assigned 

a rating, which can be used to help inform the public about 

why the ecosystem is affected and what would need to change 

in order for conditions to improve. The following indicators 

are used:

• Plankton—discrete samples for characterizations (phytoplankton versus zooplankton) and HABs

• Macroalgae—survey data

• Dissolved oxygen—continuous and discrete sampling

• Nutrient—nitrogen and phosphorus—loading values 

(based on supporting sample data)

• Water clarity and turbidity—continuous and discrete 

sampling

These indicators require data to be monitored consistently with 

proper quality assurance and over an adequate spatial distribution based on salinity gradients and waterbody features. The 

assessment also requires planning for the collection of related 

information, including land-use information, drainage areas, 

and elevation characteristics. Continued monitoring for the 

trophic state indicators (TSIs) could help establish trends that 

can be used to provide updates to the community as infrastructure, resiliency, and stormwater best management practices 

(BMPs) that include green infrastructure are implemented.

Using a set of criteria similar to the TSIs, the University 

of Maryland developed metrics by which estuaries could be 

reported in estuary report cards (Williams and others, 2009). 

Examples of these report cards have been created for watersheds of the Long Island Sound (University of Maryland 

Center for Environmental Science, 2015b) and the Chesapeake 

Bay (University of Maryland Center for Environmental Science, 2015a). By following the guidance in the “Sampling and 

data analysis protocols for Mid-Atlantic tidal tributary indicators” (EcoCheck, 2011), the three Reserve regions—western 

bays (Hempstead and South Oyster Bays), Great South Bay, 

and eastern bays (Moriches, Quantuck, and Shinnecock 

Bays)—could be divided into sections based on salinity gradient from start-of-flow through the watershed to the bays. It is 

likely that such a report card would result in low grades (on 

the scale A–D or F) for all three regions because of overall 

high levels of nutrient loading, documented areas of hypoxia, 

increased harmful algal blooms in the Great South Bay and 

eastern bays, and high amounts of Ulva in the western bays. A 

similar approach is used by the Gobler Laboratory of SoMAS 

to provide a water quality index that provides a weekly status 

of the waters around Long Island (News12, 2016) by using 

real-time water-quality monitoring data and grab samples 

collected for harmful algae colony counts. Incorporating loading estimates and available data on SAV would allow for the 

creation of a comprehensive report card for the Reserve and 

would be a useful tool for community outreach and citizen 

science engagement.

Low-Impact Development and Best 

Management Practices

Low-impact development, including green infrastructure 

(EPA, 2017c), and nonpoint or stormwater BMP implementation across Long Island generally occurs as individual projects 

on a small scale within a limited recharge zone (for example, 

storm drain inserts or roadway bioswales). Resources for 

proper design and implementation of stormwater management have been developed by the NYSDEC (NYSDEC, 2015; 

http://www.dec.ny.gov/chemical/96777.html), and effective 

monitoring before and after implementation is important to 

understanding successful implementation. Although results 

from a project can be used to support BMP use in other areas, 

little coordination is apparent at this stage. Small-scale projects are not likely to change the overall health of the Reserve 

ecosystem; however, monitoring the water and infrastructure 

function of these systems before and after project implementation is key to determining their overall contributions to 

the Reserve. Data and information about BMPs being used 

throughout the world can be found at the International Stormwater Best Management Practices Database website 

(http://www.bmpdatabase.org/index.htm).

Currently (2017), BMP projects have been established in 

the following areas: Nassau County recharge basins, though 

a shortage of resources does not allow for upkeep of the sediment traps and oil filters; storm drain inserts in the Village of 

Freeport; and bioswales along the roadways of Cedar Creek 

County Park within the Cedar Creek Water Pollution Control Plant. Although grants available from the EPA and other 

sources typically cover the cost of planning, construction, and 

limited maintenance, water and ecological monitoring and 

long-term maintenance are often not in place, in which case 

efficacy cannot be established over time. Further, water-quality and ecological-health monitoring of BMPs in other regions 

can be used as examples for the monitoring in the Reserve. 

Two examples of regional programs can be found in the Great 

Lakes and the Chesapeake Bay:

• Great Lakes

• The Great Lakes Coastal Resilience has cataloged 

initiatives and guidance for developing and monitoring based on issues and infrastructure type (Great 

Lakes Coastal Resilience, 2013).

• The Great Lakes Restoration Initiative is a partnership among 16 Federal agencies aimed at accelerating the revitalization of the Great Lakes. Under this 

program, the EPA and USGS develop monitoring 

programs in collaboration with States and municipalities and implement citywide BMP and green 

infrastructure projects (Great Lakes Restoration 

Initiative, 2016).
18 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

• Chesapeake Bay

• The Chesapeake Bay Program has developed guidance that includes considerations across jurisdictional boundaries (in the case of the Reserve, towns 

and counties) for BMP implementation and monitoring in urban, agricultural, and mixed-use watersheds 

(Chesapeake Bay Program, 2012).

One strategy that has shown to be effective (with proper 

guidance and protocols) for monitoring basic constituents is 

coordination with community volunteers participating in citizen science (such as school or Boy and Girl Scout groups in 

the A Day in the Life program [http://www.portaltodiscovery.

org/aday/about.htm]). 

Citizen Science

Volunteer monitoring programs provide not only data 

important for indicating areas of potential concern but also an 

educational experience for those involved. Citizen science can 

be used to cover data gaps of basic water-quality constituents 

(for example, dissolved oxygen monitoring along a tributary 

with a declining fish population) and conduct surveys (for 

example, identifying storm drains that could be effective sites 

for green infrastructure) when Federal, State, and (or) local 

government resources are limited or monitoring frequencies 

are inadequate for answering specific questions about the 

waters. The goals of a citizen monitoring program—to provide 

a basic understanding of water quality in a bay or directly 

inform decisions related to waterbody impairment listings—

are important considerations when choosing protocols and 

methods for collecting data. Field methods, quality assurance, 

and resources used by other groups for estuaries across Long 

Island and throughout the country can be transferable. There 

are a number of guides for citizen science monitoring, and it 

is important that an approved quality assurance project plan 

(QAPP) is followed for data to be considered for use in decision making by other organizations. Acknowledging the work 

of all groups collecting and providing data, regardless of quality, is necessary for encouraging and promoting citizen science 

in the Reserve.

Synergy Among Existing Management and 

Action Plans

Over the last 15 years, more than 30 management and 

action plans evaluating the ecological resources of the Reserve 

have been completed or are under development. These plans 

outline different issues currently facing areas of the Reserve, 

propose who can address the issues and how, and address 

areas ranging in scope from a single watershed to an entire 

bay. While some of the recommendations in these plans have 

been implemented (for example, monitoring implemented 

as a result of the recommendations in the 2000 CWRMS 

and implementation of action items in the CMP are provided 

in table 1–5), others have not, mainly because of a lack of 

resources or coordination. Many of the management plans 

have similar formats for describing issues that could be 

extrapolated to the entire Reserve. Management plans and the 

waterways they address are listed in table 2.

Many of the management and action plans integrate existing monitoring and recommend new constituents or monitoring stations be added to the current programs; however, these 

additions rely on an increase in funds through Federal or State 

grants and thus are not always implemented. This CWRMS 

serves to both consolidate recommendations and provide suggestions for coordinating current monitoring programs to align 

their respective objectives as provided by members of the PAC 

(excluding the USGS).

Purpose and Scope

The goal of a coordinated strategy is to provide a framework by which stakeholders in the Reserve can maximize efficiency, share data and knowledge, build partnerships, develop 

interdisciplinary studies, leverage existing resources to avoid 

overlap in water and ecological monitoring and research, and 

identify gaps in the knowledge and data needed for management decisions and future planning at the State and local levels. To achieve this goal, information about current monitoring 

and research efforts within the Reserve has been compiled and 

presented in this report and via an interactive mapper 

(http://www.sserwaterquality.us/map.html). This information 

was gathered from representatives of organizations working 

on resource monitoring and protection within the Reserve.

This report provides an overview of the roughly 20 water 

and ecological data collection efforts currently (2017) underway in the Reserve. The report describes the quality assurance 

and quality control procedures used in these efforts as well 

as the procedures for archiving data and metadata. Data gaps 

identified by the PAC and other stakeholders and recommendations from stakeholders for addressing the gaps are 

listed to identify monitoring needs and, in some instances, 

offer ways to integrate citizen science efforts. Also listed are 

general recommendations from stakeholders for data collection and coordination among organization and monitoring 

programs. These data gaps and recommendations are expected 

to be incorporated into a planned revision to the CMP for 

the Reserve. Lastly, this report describes the content of the 

CWRMS website and Reserve mapper and how to use them.

Resource Monitoring in the Long Island 

South Shore Estuary Reserve

Environmental data are collected throughout the Reserve 

to help address management questions regarding resources and 

can be used to establish trends in water quality, water quantity, 

or ecological conditions. The funds to maintain a monitoring 
Resource Monitoring in the Long Island South Shore Estuary Reserve 19

program or conduct research typically come from Federal, 

State, and local government sources. A list of current monitoring programs relevant to water quality of the Reserve has been 

provided by stakeholders and researchers and compiled to provide a single source of information (table 4, in back of report) 

and identify potential overlap and areas where efforts can be 

coordinated. Information about recent and ongoing programs 

is presented in figures 1 through 4 and in table 4 (in back of 

report), with additional details presented in the appendixes 

1 through 3. Ecologically relevant projects that the PAC has 

identified that may benefit from ancillary water-quality data 

are listed in table 5.

Water-quality instrumentation used to collect data and 

assess the health of the Reserve has improved and evolved 

over the past 15 years. Instrumentation has become more 

sensitive and robust, models have been created and refined 

to better simulate water-quality processes and thereby help 

users understand the sources of nutrient loads to the bays and 

tributaries, and interactive tools and mappers have become 

more functional and user friendly. A partial list (based on 

stakeholder feedback) of what is currently being used to evaluate the water-quality resources of the Reserve is presented in 

table 6.

Water-Quality and Water-Quantity Programs

Continuous and discrete data are collected throughout the 

Reserve to support a long-term assessment of the waters. The 

data inform loading and model predictions, address concerns 

over eutrophication, and help identify point and nonpoint 

sources of contamination. Although continuous measurements offer advantages over discrete sampling by capturing 

seasonal and diel variations in water-quality constituents 

at greater frequency and by detecting sudden or long-term 

changes that would otherwise not be identified, the equipment 

required for continuous monitoring is costly to install and 

maintain. Discrete sampling networks offer flexibility in the 

selection of sites and the ability to get better spatial coverage in a day, effectively providing a snapshot of water quality 

in the estuary. Discharge and stage of tributaries along with 

groundwater levels in the Reserve watershed are important for 

understanding the contributions of freshwater to the estuary. 

A comprehensive network is in place for monitoring these 

data (though additional streams and wells would improve the 

network coverage and resolution and would provide data for 

better modeling). Synchronization of the water-quality and 

water-quantity programs managed by Federal, State, Tribal, 

and local agencies and citizen and academic organizations 

around routine and event monitoring would improve efficiency 

and data coverage spatially.

Continuous Water-Quality Monitoring

1. Great South Bay Project/Observatory is a collaboration 

between the Stony Brook University School of Marine 

and Atmospheric Sciences, New York Sea Grant, and the 

New York State Department of State. Data are being collected from eight stations on the Great South Bay: Smith 

Point, Carmans River, Bellport, Blue Point, Islip, Tanner 

Park, the U.S. Coast Guard Station on Fire Island, and 

Barrett Beach on Fire Island. Instruments are deployed 

up to three months at a time, with more frequent visits 

in the summer because of heavy biofouling. The buoy, 

deployed south of Sayville in the Great South Bay, 

reports wind speed and direction, air temperature and 

humidity, photosynthetically active radiation, water 

temperature and salinity, chlorophyll a, fluorescence, 

and turbidity in conjunction with other data to inform 

the development of circulation and low-trophic-level 

models. Data from 2010–17 are available from 

(http://po.msrc.sunysb.edu/GSB/).

2. The Town of Hempstead has collected physical constituents (temperature, dissolved oxygen, salinity, turbidity, and chlorophyll a) at 6-minute intervals from East 

Rockaway Channel, at a site that coincides with the U.S. 

Geological Survey tide gage, and Wreck Lead Channel 

since 2010. Data are available by contacting the Town of 

Hempstead Department of Conservation and Waterways 

(Town of Hempstead, 2017).

3. The USGS operates water-quality monitoring stations 

to collect continuous tidal-water elevations and select 

water-quality constituents from Hog Island at Island 

Park and Reynolds Channel at Point Lookout. Waterquality constituents include water temperature, specific 

conductance (used to compute salinity), dissolved oxygen, turbidity, and chlorophyll a and are collected from 

0.5 m above the seabed; at Hog Island, pH and nitrate 

also are collected. Data are collected at 6-minute intervals (30-minute intervals for nitrate) and are available 

through the National Water Information System (NWIS) 

Web interface.

4. The Nature Conservancy (TNC) and USGS have 

deployed 20 dissolved oxygen sensors at 12 stations in 

the Great South Bay to investigate diurnal and seasonal 

variations in the hypoxic zone between Oakdale and 

Patchogue Bay, including Nicoll Bay south of Heckscher State Park up the Connetquot River. Sensors are 

0.5 meter above the seabed and record at 6-minute intervals. Each sensor is collocated with a dissolved oxygen 

sensor run by SoMAS for a different study. Contact the 

USGS New York Water Science Center, Coram office, or 

TNC for more information.

5. LIShore is a SoMAS project founded in 1998 to provide 

real-time sea and shoreline conditions for Long Island 

and has been operated in collaboration with numerous 

sponsors and partners. LIShore presently operates six 

real-time observatories across the Reserve (Shinnecock 

Inlet, Smith Point, Seaford, Merrick, Bay Park, Point 
20 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

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Hempstead

Bay

Reynolds Channel

Mill River

East Meadow

Brook

Bellmore

Creek

Massapequa

Creek

East Rockaway Inlet

Jones

Inlet

73°30'W 73°40'W

40°40'N40°35'N

South Oyster Bay

NASSAU

QUEENS

0 1.5 3 MILES0 1.5 3 KILOMETERS

ATLANTIC OCEAN

Base from U.S. Geological Survey digital data, 2016Projection: State Plane, New York, Long IslandNorth American Datum of 1983

NYSDECSoMAS

Town of Hempstead USGS

^ New site

Add constituents

Resume old program

EXPLANATION

South Shore Estuary Reserve ExtentSite TypePAC Recommendations

Figure 2. Ongoing and proposed monitoring in the western bays of the South Shore Estuary Reserve, New York. NYSDEC, New York State Department of 

Environmental Conservation; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; USGS, U.S. Geological Survey.
Resource Monitoring in the Long Island South Shore Estuary Reserve 21

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73°W 73°10'W 73°20'W

40°50'N40°40'N

SUFFOLK

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GREAT SOUTH BAY

ATLANTIC OCEAN

Base from U.S. Geological Survey digital data, 2016Projection: State Plane, New York, Long IslandNorth American Datum of 1983

Connetquot River

Carlls River

Sampawams

Creek

Green

Creek

Brown Creek

Carmans

River

Patchogue

River

Swan River Mud Creek

Beaverdam

Creek

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Inlet

Old Inlet

Chaplin Creek

^ New site

Add constituents

EXPLANATION

South Shore Estuary Reserve ExtentSite TypePAC Recommendations

NYSDECMolloy CollegeSuffolk County DHS

The Nature ConservancyUSGSSoMAS

Figure 3. Ongoing and proposed monitoring in the Great South Bay of the South Shore Estuary Reserve, New York. DHS, Department of Health Services; NYSDEC, New 

York State Department of Environmental Conservation; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; USGS, U.S. Geological Survey.
22 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

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72°30'W 72°40'W 72°50'W

40°55'N40°50'N40°45'N

ATLANTIC OCEAN

0 2 4 MILES0 2 4 KILOMETERS

Base from U.S. Geological Survey digital data, 2016Projection: State Plane, New York, Long IslandNorth American Datum of 1983

SUFFOLK

^ New site

Add constituents

EXPLANATION

South Shore Estuary Reserve ExtentSite TypePAC Recommendations

Suffolk County DHSSoMAS

USGS

Moriches Inlet

Forge River

Heady Creek

Moriches Bay

Tiana

Bay

Shinnecock Bay

Shinnecock

Inlet

Quantuck

Bay

Figure 4. Ongoing and proposed monitoring in the eastern bays of the South Shore Estuary Reserve, New York. DHS, Department of Health Services; SoMAS, Stony 

Brook University School of Marine and Atmospheric Sciences; USGS, U.S. Geological Survey.
Resource Monitoring in the Long Island South Shore Estuary Reserve 23

Table 5. List of projects relevant to water quality and ecological health ongoing or completed since 2000 in the South Shore Estuary Reserve, New York.[Names and details related to a project are provided by the responsible organization. Additional monitoring reflects needs identified by the organization or other stakeholders to improve the project outcome, interpretation, or deliverables. Reserve, South Shore Estuary Reserve; SCDPW, Suffolk County Department of Public Works; SCDHS, Suffolk County Department of Health Services; SET, surface elevation table; SC, Suffolk County; NYSDEC, New York State Department of Environmental Conservation; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; IHS, Indian Health Service; SHIN RMP, Shinnecock Tribal Lands and Bay Resources Management Plan; --, not available or not applicable]

Project Organization Level Objectives Additional moni- toring needed Collaborators Management plan Link

Marsh Restoration 

within the Reserve watershed: National Fish and Wildlife Foundation post-Hurricane Sandy grant

Suffolk County: 

SCDPW Office of Vector Control and SCDHS, Division of Water Quality

County Restore marsh tidal 

flow, improve marsh resiliency, improve flood and storm surge protection

Marsh accretion 

(SETs)

SC Parks 

Department, The Nature Conservancy, NYSDEC

Integrated Marsh 

Management under the SC Wetlands Stewardship Strategy

--

Fire Island to 

Montauk Point Reformulation Study

U.S. Army Corps of 

Engineers

Federal Natural Resources Study 

was conducted to gather current water quality and biological data from Fire Island inlet to Montauk Point

-- -- -- U.S. Army Corps of Engineers (2017); 

http://www.nan.usace.army.mil/Missions/Civil-Works/Projects-inNew-York/Fire-Island-to-Montauk-Point-Reformulation-Study/

Estuarine Eutrophication Programs National Oceanic and Atmospheric 

Administration (Office of Ocean Resources)

Federal Development of a nationwide assessment of 

estuaries to determine effect of nutrients

-- -- -- National Oceanic and Atmospheric Administration (2007); 

http://ian.umces.edu/neea/

Fire Island Characterization National Park Service Federal Characterizing Fire Island landscape and wildlife -- -- -- --

Wetland Grasses 

Survey

Great South Bay 

Audubon Society

Nonprofit Photos taken of shoreline grass loss in the Towns 

of Islip and Babylon

-- SoMAS -- --

Storm Drain Inserts Operation SPLASH Nonprofit Reduce contaminant load- ing to the bays from 

runoff

Water quality at 

drain and at outfall

SPLASH, Town 

of Hempstead

-- --

Land Use Long Island Regional Planning 

Council

Regional Develop a plan for future development in Nassau 

and Suffolk County

-- -- -- --

Various resiliency 

projects

New York State Rebuild by Design State Shoreline hardening, wetland reconstruction, 

infrastructure resiliency

-- -- -- --

Fish ladders Town of Brookhaven, Town of 

Babylon

Town Fish ladders constructed 

at Carmans River and Carlls River, plans are underway for Swan River

-- -- Carmans River 

Conservation and Management Plan

Town of Brookhaven (2013); 

http://www.brookhaven.org/portals/0/documents/planning/2013%20Carmans%20River%20Conservation%20and%20Management%20Plan.pdf

East Bay Sanitary 

Survey

Town of Hempstead Town Stop Throwing Out Pollutants (STOP) and 

E-Cycle

-- -- -- --
24 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 5. List of projects relevant to water quality and ecological health ongoing or completed since 2000 in the South Shore Estuary Reserve, New York.—Continued [Names and details related to a project are provided by the responsible organization. Additional monitoring reflects needs identified by the organization or other stakeholders to improve the project outcome, interpretation, or deliverables. Reserve, South Shore Estuary Reserve; SCDPW, Suffolk County Department of Public Works; SCDHS, Suffolk County Department of Health Services; SET, surface elevation table; SC, Suffolk County; NYSDEC, New York State Department of Environmental Conservation; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; IHS, Indian Health Service; SHIN RMP, Shinnecock Tribal Lands and Bay Resources Management Plan; --, not available or not applicable] Project Organization Level Objectives Additional moni- toring needed Collaborators Management plan Link Hard Clam Grow Out Program Town of Hempstead Town Increase clam populations -- -- -- -- Various water qual- ity and ecologi- cal studies Town of Hempstead Town -- -- NYSDEC, DOS -- Town of Hempstead (2012); https://www.dos.ny.gov/opd/sser/pdf/T%20Hempstead%20 Water%20Quality%20Report%201975-2012%20FINAL.pdf Marsh Restoration Shinnecock Nation Tribal Restore flow to marshes and reduce mosquito population -- NYSDEC, DOS, Suffolk County SHIN RMP -- Beach replenish- ment Shinnecock Nation Tribal Restore beach on western shore of peninsula and protect cemetary -- DOS, IHS SHIN RMP -- Oyster farming Shinnecock Nation Tribal Preserve culture and economy through aquaculture -- NYSDEC SHIN RMP -- Wastewater infrastructure investigation Shinnecock Nation Tribal Reduce impact to ground- water and bay through improved wastewater infrastructure -- IHS SHIN RMP --
Resource Monitoring in the Long Island South Shore Estuary Reserve 25

Table 6. Partial list of field equipment used or deployed for water-quality monitoring in the South Shore Estuary Reserve, New York.

[Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. SoMAS, Stony Brook 

University School of Marine and Atmospheric Sciences; USGS, U.S. Geological Survey]

Organization Field equipment Constituents

SoMAS Great South Bay buoy #1: designed and built at SoMAS 

Ocean Instrument Laboratory

WEATHER, AT, WT, SAL, CHL, TURB, PAR

SoMAS Tide and water temperature stations: designed and built at 

SoMAS Ocean Instrument Laboratory

WL, WT

SoMAS Shoreline camera systems: designed and built at SoMAS 

Ocean Instrument Laboratory

PHOTO

SoMAS and 

Town of Hempstead

WETLabs WQM WT, DO, SAL, CHL, TURB

SoMAS Biospherical Instruments QSR–2150 PAR

SoMAS Sea-Bird SBE16 WT, SAL, CHL, TURB, WL

SoMAS Davis Vantage VUE WEATHER, AT

SoMAS RM Young Marine Wind Monitor 05106 WEATHER

SoMAS Sea-Bird SBE37 MicroCAT WT, SAL 

SoMAS Vaisala HMP-155 WEATHER

SoMAS WETLabs ECO FLNTU CHL, TURB

USGS YSI 6600 WT, SAL, pH, TURB, DO, CHL, DEPTH

USGS EXO2 WT, SAL, pH, TURB, DO, CHL, DEPTH, fDOM

USGS AquaTroll DEPTH, WT, SAL

USGS Satlantic SUNA NO3

Suffolk County YSI 556 Multi Probe System WT, SAL

Suffolk County YSI Pro Plus DO

Suffolk County Secchi disk CLAR

Town of Hempstead YSI sonde WT, SAL, pH, DO

Molloy College Weather station WEATHER

Lookout) and is currently funded to expand the Shinnecock Inlet site and add one new station at Southampton. In addition to operating the observatories, LIShore 

provides operational and telemetry support for the 

Great South Bay buoy, the Bellport observatory of the 

Great South Bay Project, and the Town of Hempstead 

Oceanside water-quality station. Public data from five 

USGS stations are mirrored on the LIShore website at a 

sponsor’s request (Town of Hempstead). Available data 

include water level; water quality (water temperature, 

turbidity, dissolved oxygen, salinity, and chlorophyll a); 

weather; waves and currents (from historic installations); 

and panoramic image sets, panoramas, and time-lapse 

photography of shorelines and inlets. Data are available 

at http://www.lishore.org/.

Discrete Water-Quality Monitoring

1. The Suffolk County Department of Health Services 

Office of Ecology monitors water quality (physical, 

chemical, and biological constituents) on a monthly 

basis at sites in Beaverdam Creek, Yaphank Creek, Little 

Neck Creek, Carmans River, Connetquot River, Forge 

River, Grand Canal, Patchogue River, Poospatuck Creek, 

Willets Creek, and Carlls River, as well as sampling in 

open water in the Suffolk County bays and inlets of the 

Reserve. The data for roughly 50 sites are available at 

and

https://gisportal.suffolkcountyny.gov/gis/home/item.html

?id=a4793d074dae4c95b43ac95864f0d7a0

http://www.sserwaterquality.us. Constituents include 

temperature, light penetration, dissolved oxygen, salinity, conductivity, nutrients (various forms of nitrogen and 

phosphorous), fecal indicator bacteria, suspended solids, 

chlorophyll a, and phytoplankton. Samples are analyzed 

by the SCDHS laboratory; methods are approved by the 

U.S. Environmental Protection Agency (EPA) and comparable to the Town of Hempstead sampling methods—

though analyte suite and reporting requirements vary.

2. The Town of Hempstead monitors water quality throughout Hempstead Bay. Samples are analyzed for physical 
26 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

constituents, nutrients, metals, organic compounds, and 

coliforms. Samples are collected monthly from 40 sites 

and analyzed at the Town of Hempstead laboratory. Data 

are available by contacting the town’s Department of 

Conservation and Waterways.

3. The Center for Environmental Research and Coastal 

Oceans Monitoring (CERCOM) at Molloy College tests 

15 sites in Great South Bay to monitor for dissolved 

oxygen, pH, salinity, clarity, chlorophyll a, and temperature. This monitoring program has been conducted since 

2002 (initially in conjunction with Dowling College) on 

a weekly basis from Memorial Day to Labor Day. These 

constituents supplement the SCDHS sampling data for 

Great South Bay (Tanacredi, 2015).

4. The Shinnecock Environmental Department is developing a nearshore water-quality program for physical 

constituents, phytoplankton, and fecal indicator bacteria 

around the Shinnecock peninsula to support oyster farming (in cooperation with Cornell Cooperative Extension). 

Water temperature, pH, and dissolved oxygen data have 

been collected since 2014.

5. The New York State Department of Environmental 

Conservation Division of Water assessed water quality 

and ecologic diversity as part of the statewide Rotating Integrated Basin Studies (commonly referred to as 

RIBS) program at the following Reserve tributaries during 2013–15: Carlls River, Carmans River, Connetquot 

Brook, and Massapequa Creek. Patchogue River, Sampawams Creek, and Swan River have not been sampled 

under Rotating Integrated Basin Studies since the 2000 

Coordinated Water Resources Monitoring Strategy was 

drafted. This network could be supplemented by assessing additional streams according to the same methods, 

including sampling at 5-year intervals, and would provide additional information on ecosystem services of the 

Reserve. Data are available through the Water Quality 

Portal (WQP) or by contacting NYSDEC (n.d.[c]).

6. The NYSDEC Division of Marine Resources monitors 

water quality (fecal coliform) in designated shellfish 

areas throughout the Reserve and determines whether an 

area is open for harvest (commercially or recreationally).

7. The SCDHS Office of Ecology and the Nassau County 

Department of Health test water from public bathing 

beaches for enterococci on a weekly basis from May to 

September (with sample collection in Nassau County 

conducted by the Towns of Hempstead and Oyster Bay). 

Data are available by contacting the SCDHS Office of 

Ecology.

8. The New York State Office of Parks, Recreation, and 

Historical Preservation tests water at public bathing 

beaches for enterococci on a weekly basis from May to 

September and posts alerts at parks if water is found to 

have unsafe levels of bacteria. Data are available from 

the Office of Parks, Recreation, and Historic Preservation or NYSDEC.

9. The USGS collects water samples at the Carmans River 

streamgage for nutrient and major ion (such as iron, 

manganese, chloride) analyses. The current study has 

been ongoing since 2015, and previous studies date 

to the 1970s. Discrete water-quality data collected at 

Carmans River and other tributaries to the Reserve are 

available through NWIS (https://nwis.waterdata.usgs.

gov/ny/nwis/qwdata).

10. The National Oceanic and Atmospheric Administration 

(2017a) maintains an ocean monitoring buoy (water temperature, current, mean wave direction, wave period and 

height, and meteorological constituents) in the Atlantic Ocean, 35 miles south of the Fire Island Inlet, that 

provides conditions of water circulating into the bays 

through the Reserve inlets (NOAA, 2017a).

11. Operation SPLASH collects physical water-quality 

constituents (pH, dissolved oxygen, salinity, and water 

temperature) from select locations during litter removal 

efforts in Hempstead Bay. Data on type and quantity of 

litter removed from the western bays of the Reserve are 

available by contacting the Operation SPLASH office 

(Operation Splash, 2016).

12. The New York State Marine Education Association runs 

the South Shore Estuary Learning Facilitator Program, 

which is designed to provide resources to student 

and community groups in the monitoring of physical 

water-quality constituents. This program could either 

be expanded to include more schools or team up with 

A Day in the Life to increase the number of streams and 

frequency of data collection as part of a larger citizen 

science effort.

13. A Day in the Life is a nonprofit citizen organization 

that teaches high school students about water quality 

and ecology through field experience. Tributaries to the 

Reserve used by A Day in the Life include the Carlls 

River (5 sites along the river), Carmans River (21 sites), 

Connetquot River (5 sites), and Green Creek (4 sites). 

Sites are visited once per year and sampled for pH, 

salinity, dissolved oxygen, turbidity, water temperature, 

and, during some outings, for nutrients and macroinvertebrates. Pictures of the site are often included in the 

metadata (A Day in the Life, n.d.).

Water-Quantity Monitoring

1. The USGS monitors the hydrodynamics of the Reserve 

through a series of streamgages, tidal gages, and groundwater wells.
Resource Monitoring in the Long Island South Shore Estuary Reserve 27

A. The streamgaging network includes nine tributaries to the Reserve. Continuous data are available at 

East Meadow Brook, Bellmore Creek, Sampawams 

Creek, and Swan River, and, in real time, for sites 

on Massapequa Creek, Valley Stream, Carlls River, 

Connetquot Brook (two sites), and Carmans River. 

In the modeling of contaminant transport, these measurements provide data necessary for determining 

loading of surface-water and groundwater contributions to the Reserve.

B. Tidal gaging stations in the Reserve at Shinnecock Bay, Moriches Bay (East Moriches), Great 

South Bay (Watch Hill and Lindenhurst), Hudson 

Bay (Freeport), and at the water-quality stations 

in Reynolds Channel and Hog Island Channel 

provide continuous, real-time records of tidal 

data and an early warning of potential flooding 

for emergency responders. Data for all sites are 

available at https://waterdata.usgs.gov/ny/nwis/

current/?type=tidal&group_key=basin_cd.

C. Groundwater levels within the Reserve watershed boundaries are collected on a monthly basis 

(50 wells) and annual basis (65 wells) to develop 

water-table and depth-to-groundwater maps for 

Nassau and Suffolk Counties to inform models and 

provide information on aquifer response to weather 

conditions (such as drought).

2. Suffolk County monitors the hydrodynamics of the 

Reserve through a series of streamgages and groundwater wells.

A. Streamflow is monitored at nine tributaries to the 

Reserve, some of which are also a part of the USGS 

streamgaging network. Sites include Beaverdam 

Creek, Carlls River, Carmans River, Connetquot 

River, Forge River, Patchogue River, Poospatuck 

Creek, Wills Creek, and Yaphank Creek. Streamflow 

measurements are collected monthly from these 

tributaries.

B. Groundwater levels are collected monthly from 

wells within the Reserve watershed. Some wells 

overlap with the USGS groundwater-level network. 

Data are used to generate water-table and depth-togroundwater maps for Suffolk County.

3. The Town of Hempstead, in cooperation with LIShore, 

maintains tidal gaging stations at Seamans Neck Park 

(Seaford), Nicks Point (Merrick), and at the police dock 

in Mill River (Bay Park). Data for the all the sea, inlet 

and bay conditions for Long Island are collected continuously and available online at http://www.lishore.org/.

Biological Monitoring and Surveys

Ecology in the Reserve is assessed to various degrees 

by various agencies, academics, and volunteer organizations. 

Concerns over habitat loss, shellfish population decline, and 

hypoxic zones over the past decade have spurred additional 

monitoring and restoration efforts. However, coordination 

among the biological surveys and restoration projects and the 

water-quality monitoring projects does not always occur.

Vertebrates and Invertebrates

1. The NYSDEC and SoMAS conduct surveys of Callinectes sapidus (blue crab) populations throughout the 

Reserve.

2. NOAA has collected mussels and oysters as part of Mussel Watch (part of the larger National Status and Trends 

program) since 1986. The program has three sites in the 

Reserve that are sampled every 5–10 years. Bivalve tissue analysis includes polychlorinated biphenyls (PCBs), 

polycyclic aromatic hydrocarbons (PAHs), metals, and 

other primary pollutants (NOAA, 2017b).

3. The Shinnecock Tribe and Cornell Cooperative Extension assess the health of the oyster population around 

the Shinnecock Tribal lands of the Shinnecock Bay. The 

oysters are seeded and cultivated onsite, though concern 

over poor water quality in the western portion of the bay 

is growing as algal blooms become more frequent.

4. The Towns of Hempstead and Southampton each have 

shellfish programs, which may include hatcheries and 

permitting for recreational and commercial harvesting. 

The Town of Islip hatchery is now operated by Great 

Atlantic Shellfish Farms. Water-quality monitoring is 

limited to physical constituents within the hatchery.

5. The Center for Environmental Research and Coastal 

Oceans Monitoring (CERCOM) conducts horseshoe 

crab surveys at 44 locations in the Reserve to track 

declining populations. Harvesting for bait and blood and 

changes in water quality are believed to be the leading 

factors affecting populations. Climate change may also 

be a cause of declining populations. Tissue health studies 

have also been conducted in the Reserve. Data are available by contacting CERCOM (2017).

6. The NYSDEC Division of Water’s Stream Biomonitoring Unit assesses macroinvertebrates as indicators of 

water quality (sentinels) at locations in the Reserve that 

cover most sites recommended in the 2000 CWRMS 

(NYSDEC, 2016a).

7. Cornell Cooperative Extension and the NYSDEC 

Division of Marine Resources conduct annual surveys 

for spawning horseshoe crabs at beaches throughout 
28 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

the Reserve. Data are collected to determine spawning 

abundance, size, and sex between May and July and are 

available by contacting the NYSDEC Division of Marine 

Resources.

8. The NPS runs a volunteer program to tag and track 

horseshoe crabs on the bay side of Fire Island National 

Seashore. Data from this program inform wildlife management decisions for the NPS and NYSDEC.

9. The NYS Office of Parks, Recreation, and Historic Preservation monitors trout in the Connetquot River, with a 

hatchery in Connetquot State Park that was reopened in 

2015 after being upgraded to a biosecure facility.

Microalgae and Macroalgae

1. SoMAS and the NYSDEC have increased monitoring of 

harmful algal blooms—species classification and toxin 

analysis—at three locations in Shinnecock Bay as part 

of the Marine Biotoxin Monitoring Program (NYSDEC, 

n.d.[a]). These data are being used to better understand 

the factors leading to a bloom and the production of 

toxins and their effects on wildlife (both aquatic and up 

the food chain) (NYSDEC, n.d.[a]). Data are available 

through several publications and by contacting SoMAS 

(Christopher Gobler) (The Gobler Laboratory, n.d.).

2. Cornell Cooperative Extension has mapped locations 

and monitors the health of submerged aquatic vegetation, such as eelgrass, throughout the Reserve and works 

with Suffolk County to plant eelgrass beds in the Great 

South Bay and the eastern bays. Maps of the SAV beds 

are available on Cornell Cooperative website 

(http://www.seagrassli.org/).

3. Cornell Cooperative Extension and SoMAS study 

concentrations and the classification of phytoplankton 

in the Reserve. Chlorophyll a concentrations are used as 

a proxy for phytoplankton concentration and are part of 

several water-quality monitoring programs.

4. The Town of Hempstead has been tracking Ulva washing 

up in large quantities, which is believed to be related to 

the high nitrogen loading from tributaries and effluent 

from the Bay Park Sewage Treatment Plant (STP) outfall 

in Hempstead Bay.

Wildlife

1. Long Island Audubon Society chapters host bird counts 

at locations throughout the Reserve, in particular at Captree State Park and Baldwin Bay as part of the Christmas 

Count, in which counts are tabulated across the country. 

Data are available through the National Audubon Society 

Christmas Bird Count web page (http://netapp.audubon.

org/cbcobservation/) or by contacting a local chapter. 

Records are available for every year since 1900.

Invasive Species

1. The Seatuck Environmental Association surveys 

Phragmites in wetlands around the Reserve as part of an 

educational outreach program.

2. The NPS, U.S. Fish and Wildlife Service (FWS), 

NYSDEC, and NYS Office of Parks, Recreation, and 

Historical Preservation have been tracking invasive 

beetles—one of the management priorities over the past 

decade. Several species currently exist on Long Island 

and have affected trees within the Reserve watershed 

(for example, thousands of pine trees in Connetquot 

State Park have been cut down to prevent the spread of 

Dendroctonus frontalis [southern pine beetle]).

Sediment-Quality Monitoring

Marsh and bed sediment provide the substrate necessary 

for seagrasses, shellfish, and other organisms to live. However, sediment is also a sink for anthropogenic contaminants 

introduced to the water column by point and nonpoint sources. 

There have been few comprehensive sediment-quality monitoring programs or studies conducted in the Reserve, but those 

that do exist evaluate physical properties and offer insight into 

the fate and transport of contaminants in select areas. More 

studies are needed to understand sediment dynamics, contaminant degradation, and nutrient flux throughout the Reserve and 

to properly assess any effects that reductions of wastewater 

loading to groundwater may have in the water column.

1. SoMAS studies bed-sediment quality in Hempstead Bay. 

SoMAS, in cooperation with the Town of Hempstead 

Department of Conservation and Waterways, undertook 

a comprehensive sampling effort to assess novel wastewater tracer compounds (quaternary ammonium compounds) and metals in grab (top 5 cm) and core samples 

collected during 2011–13—before and after Hurricane 

Sandy. Data are available in a publication by Doherty 

and Brownawell (2013) and by contacting SoMAS 

(Bruce Brownawell). 

2. NOAA collects sediment at sites sampled for shellfish as 

part of the Mussel Watch program—sediment samples 

are analyzed for PCBs, PAHs, metals, and other primary 

pollutants. Data are available at NOAA’s National Status 

and Trends web page (https://products.coastalscience.

noaa.gov/collections/ltmonitoring/nsandt/default.aspx).

3. The USGS and Suffolk County Vector Control assess 

sediment and water from marshlands along the south 

shore of Suffolk County for pyrethroid and other 
Quality Assurance and Quality Control, Metadata, and Data Archives 29

insecticide residues following applications targeting 

adult or larvae mosquitoes.

4. The Nature Conservancy and NPS established surface elevation tables (SETs) in marshes throughout 

the Reserve to track accretion or erosion of sediment 

from shoreline marshes and marsh islands. The Nature 

Conservancy sites include North Green Sedge, Lawrence 

Marsh, and Pine Neck. The NPS sites include Old Inlet, 

Great Gun, and Watch Hill.

Atmospheric Monitoring

Maintaining weather and long-term climate data is important for correlating changes in water quality (for example, pH 

and water temperature) and sea-level rise. Air-quality monitoring in the Reserve is limited and unsystematic. A program to 

assess nitrogen in air (those viable with current technology) 

and precipitation, as well as other pollutant concentrations 

within the Reserve boundaries, would inform models where 

nitrogen loading is estimated to be a sizeable part of the overall load through deposition.

1. The National Weather Service maintains weather stations 

at Upton, West Sayville (CERCOM), and Long Beach 

(Town of Hempstead) for real-time monitoring of air 

temperature, wind speed, and precipitation. Data are 

necessary for forecasting and are available through the 

NOAA website (https://www.ncdc.noaa.gov/data-access/

land-based-station-data).

2. A USGS real-time water-quality monitoring gage 

at Reynolds Channel records the following weather 

constituents: precipitation, wind speed, wind direction, 

temperature, humidity, and barometric pressure. Data are 

collected at 6-minute intervals.

3. LIShore observatories at Merrick, Smith Point, and Shinnecock Inlet record the following weather constituents: 

precipitation, wind speed, wind direction, temperature, 

humidity, and barometric pressure. Data are collected at 

5-minute intervals at Merrick and Shinnecock and at a 

1-minute interval at Smith Point.

Quality Assurance and Quality Control, 

Metadata, and Data Archives

Documenting the level to which field protocols and laboratory methods are implemented during collection and analysis 

of environmental data is an important component of determining data reliability. It is critical to preserve information 

about quality assurance and quality control (QA/QC) methods 

from all studies, analyses, monitoring programs, and projects. 

Any associated QA/QC data should be incorporated into the 

metadata. Metadata associated with water or biological samples collected or surveys conducted should also include references to methods of collection and analysis, and the metadata 

should be provided with the data release. Lastly, archiving 

data and metadata as a complete dataset in a safe and accessible digital repository is necessary, and though data storage and 

dissemination can be challenging with limited resources, tools 

have been developed by the Federal government to ensure 

these and other data can be preserved in perpetuity.

Quality Assurance and Quality Control

The extent to which field and laboratory protocols incorporate quality assurances depends on the available resources, 

project objective, and personnel experience and training. 

Most Federal, State, and local government water-quality 

monitoring follows established protocols for field procedures 

and laboratory methods. These established protocols ensure 

that the quality of data meets the expectations of lawmakers 

and other stakeholders providing funds for assessing issues 

concerning human and ecological health within the Reserve. 

Academic and some nonprofit organizations typically have 

research-based quality control and internal checks that can 

provide high-quality data, and it is important to maintain these 

records (in addition to what is required by those sponsoring 

the monitoring) so that the data can be used with confidence. 

Many of the accepted procedures for preventing contamination of samples, collecting the proper number of quality 

control samples (replicates, blanks, spikes), identifying issues 

with sampling equipment, and properly calibrating and logging instruments are found in U.S. Environmental Protection 

Agency guidelines (EPA, 2014, 2016) and summarized in the 

2000 Coordinated Water Resources Monitoring Strategy Current QA/QC protocols followed by organizations within the 

Reserve are presented in table 4 (in back of report). A summary of the information that would be useful for tracking and 

monitoring QA/QC should include the following:

• Protocol(s) followed (for example, instruction manuals 

or methods paper)

• Logs of field checks of constituents with calibrated 

monitors

• Documentation of corrections applied to data based on 

internal checks and procedures for data corrections (for 

example, formulas used to calculate value offsets when 

biofouling of a water-quality instrument caused a drift 

in data)

Since 2000, and with the implementation of the 2001 

Comprehensive Management Plan, nongovernmental organizations have been collecting and providing a growing volume 

of the data necessary for identifying and understanding issues 

of poor water quality in bays and tributaries. Integrating the 

variety of data that are collected via different methods and 

protocols can be facilitated by first identifying the level of 
30 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

QA/QC and scientific rigor that went into collection, analysis, 

and interpretation. In general, the New York State Department 

of Environmental Conservation does not use citizen science 

or academic research data for regulatory purposes unless data 

collection is performed under a quality assurance project plan 

with analyses being conducted by an approved laboratory.

Quality Assurance Project Plans

A QAPP describes the necessary quality assurance 

procedures, quality control activities, and other technical 

activities that will be implemented as part of a specific project 

or program. The data collection procedures and training of 

responsible parties documented in a QAPP are reviewed by the 

EPA and (or) the State to ensure sufficient quality to meet project objectives (EPA, 2002). Developing a versatile QAPP for 

groups interested in filling data gaps but possessing varying 

degrees of expertise and resources can be challenging. Each 

organization receiving EPA or State funding for environmental 

monitoring is required to have a QAPP, or QAPP-like document, submitted prior to beginning the project. Selecting the 

appropriate protocol for collecting field data is important for 

citizen science and nonprofit groups interested in providing 

supplemental data to established monitoring networks, and 

resources exist to assist these organizations, which may find 

developing an effective protocol challenging without expert 

guidance. Therefore, having a standardized template tailored 

to the environmental aspects (for example, hydrology or ecology) of the Reserve could help save time and resources.

“The General QAPP for Long Island Sound Volunteer 

Coastal Monitoring” (Vaudrey and Gallagher, 2013) provides 

a template that organizations interested in collecting waterquality or ecological data within the Long Island Sound can 

use to satisfy one of the requirements for funding through 

State and EPA grants. The general QAPP provides the necessary components for sampling within an estuarine and 

freshwater tributary: project management, data acquisition, 

assessment and oversight, and data validation and usability. 

This QAPP could be adapted for use within the Reserve. Other 

examples of volunteer monitoring programs with QAPPs that 

could serve as examples for water-quality monitoring within 

the Reserve include the following:

• Friends of the Bay (Oyster Bay, New York) conducts 

water-quality and ecological assessments in streams 

and the open waters of Cold Spring Harbor and Oyster 

Bay following a pair of approved QAPPs (Friends of 

the Bay, 2006; Fuss & O’Neill, Inc., 2007). Following these protocols and ensuring proper QA/QC has 

allowed for results to contribute to a watershed action 

plan and annual state of the watershed reports.

• The Hempstead Harbor Protection Committee (Hempstead, N.Y.) coordinates watershed protection plans and 

water-quality sampling on behalf of the municipalities 

surrounding Hempstead Harbor (Hempstead Harbor 

Protection Committee, 2017).

• Save the Sound (New Haven, Connecticut) is working 

on a more general water-quality sampling protocol than 

their current QAPP (Connecticut Fund for the Environment, 2016) for their volunteers that offers several 

methods for collections but has a common method for 

reporting and ensuring proper QA/QC standards are 

practiced.

• The River Project (New York City, N.Y.) has a citizen 

science project for enterococci sampling in the New 

York-New Jersey Harbor Estuary Program—weekly 

samples are collected following an established QAPP 

and EPA-approved methods and are used to determine 

fecal indicator bacteria concentrations near permitted 

combined sewer overflows and storm drain outfalls.

From these and other volunteer monitoring programs, mediaspecific documentation can be generated and stored at the 

Reserve Office for incorporation into project proposals.

Proposed Ranking of Data

Qualifying data on the basis of the procedures and methods implemented does not imply data without the highest level 

of QA/QC are not useful; rather, qualification is a metric to 

suggest a way in which data could be used. A tiered approach 

has been adopted by some State and Federal agencies to indicate the extent to which records have been kept and calibrations performed and the quality of analyses. Efforts are underway in other estuary programs (for example, the Long Island 

Sound Study [LISS] and Peconic Estuary Program [PEP]) 

to implement a tiered system to help describe the quality of 

data collected by all organizations. Given that data collection 

by citizen science groups throughout Long Island typically 

is not coordinated with respect to standardized methods, the 

members of the Project Advisory Committee recommend that 

the Reserve Office citizen science coordinator directly interact 

with outreach coordinators from the LISS, PEP, and other 

groups operating outside the umbrella of these organizations 

to ensure standardized and approved options are available to 

all groups wishing to collect the highest quality data for their 

waterbody or ecosystem of interest.

One example that could be adopted by the Reserve Office 

for data collected within the Reserve comes from the Indiana 

Department of Environmental Management, which has created 

a guidance document for data that are being accepted into its 

water-quality database program (Arthur, 2015). A tiered system allows for data to be assigned a rank, and the system can 

be applicable to past, current, and future datasets. It is important to note that the datasets, not the organizations, are ranked. 

This scheme of ranking datasets in tiers 1 through 3 has been 

applied to the datasets indicated by Reserve stakeholders 

whose monitoring programs are presented on the South Shore 

Estuary Reserve CWRMS website.

• Tier 1 represents data of unknown quality, mainly 

because metadata or QC data do not accompany the 
Quality Assurance and Quality Control, Metadata, and Data Archives 31

records or because an approved QAPP (or QAPPlike document) was not used in field collection and 

analyses. Examples include results from a citizen science colorimetric test kit of water quality and wildlife 

surveys by volunteers organized by a group that does 

not follow an established protocol. These data are usually collected by groups interested in providing basic 

information about a system and lacking the resources, 

expertise, or need to follow advanced protocols for 

field data collection and methods of analysis approved 

by a regulatory agency. These data are informational 

and not legally defensible.

• Tier 2 represents data collected by groups or agencies 

that follow an approved QAPP but use research-level 

or unapproved methods for analyses. Examples include 

academic research that was collected and published 

in a thesis and data collected and analyzed by volunteer organizations with an approved QAPP that used 

a handheld spectrofluorometer following methods of 

EPA-approved test kits. These data could be used to 

drive additional research and supplement modeling 

efforts but are not necessarily legally defensible or 

usable for policy.

• Tier 3 represents data that have been collected, processed, and analyzed according to an approved EPA 

or other State or Federal method that has undergone 

intensive review within the discipline. All data and 

metadata are quality assured and records are archived. 

These data can be used to support modeling efforts; 

write policy, human and environmental thresholds 

(such as maximum contaminant limits), and loading regulations (such as total maximum daily loads 

[TMDLs]); and are legally defensible.

Included in table 4 (in back of report) are ranked values based 

on this tiered approach, and these ranks are included in the 

attribute table of the programs displayed on the South Shore 

Estuary Reserve CWRMS mapper (http://www.sserwaterquality.us/map.html).

Optimizing QA/QC can be challenging—the amount 

of quality control needed to reach the desired level of confidence and statistical deviation can be calculated on the basis 

of sample size and distribution (Wilde, 2006) and can easily increase the project budget beyond means. Budget and 

resource restrictions typically limit the quality of data that 

can be collected and are particularly challenging for citizen 

science organizations. For this reason, procedures such as 

collecting 5 percent of the sample set for quality control, as 

blanks, replicates, and other checks, are established for most 

types of assessments implemented. Advanced environmental 

monitoring equipment is expensive, as is laboratory analysis 

by EPA-approved facilities. Equipment loaner programs, such 

as the newly initiated EPA citizen science loaner program 

(https://www.epa.gov/citizen-science/additional-resourcescitizen-science-environmental-protection), could be useful to 

help establish a monitoring program for organizations looking 

to address a specific data gap. Facilitating the loaner program 

process, along with providing guidance on use and calibration, 

would improve the usability of data collected and potentially 

encourage greater participation.

Defining and Standardizing Metadata

Proper collection and association of metadata would 

improve data usage now and in the future, especially as field 

crews and project leads change and projects end. This is 

particularly important for government agencies because data 

are typically used to make management and policy decisions. 

Monitoring programs by agencies that do not follow a QAPP 

should follow published protocols or manuals, which can 

be modeled from State and Federal data collection agencies 

(EPA, 2002). Though typically included in a data collection 

QAPP and protocol, at a minimum, the following information about sample locations, sample collection, and sample 

analysis must be recorded and stored with the data to ensure 

data usability:

1. Field information

A. Organization site name

B. Global Positioning System (GPS) coordinates and 

datum

C. Monitoring equipment

I. Make, model, and serial number(s)

II. Calibration and service notes, including date 

and time performed

D. Project coordinator or principle investigator with 

contact information

E. Field crew names

F. File names of all site pictures (even if they are not to 

be released with data)

G. Weather (as bad weather may influence sampling 

conditions)

H. Sea, bay, or stream conditions (if applicable)

I. Site identifiers of any other sampling programs collocated at site

2. Sample collection

A. Make and model number of sampling equipment

B. Type of samples collected

C. Lot numbers of any preservatives used (for example, 

dropper acid for vials of volatile organic compounds)
32 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

D. QAPP and (or) protocol/procedure(s) followed

E. Chain of custody documentation

3. Sample analysis

A. Sampling processing and hold time information

B. Document(s) or procedure(s) followed

C. EPA method number or equivalent (if applicable)

Electronic Field Forms

Paper field forms listing the required information are 

typically used; however, electronic field form applications 

are available for free or are easy to develop and use on 

smartphones or portable field devices. The main advantage of 

these applications is the intrinsic acquisition of metadata from 

the device operating system, including GPS and other active 

tools that can be standardized to reduce the burden of manual 

entry by the field crew. One example is Open Data Kit 

(https://opendatakit.org/). Applications such as this allow 

most field tablets or smartphones to be used to record field 

data, with the options of automatically populating fields 

with common entries and selecting entries from dropdown 

menus, expediting the data-entry process and minimizing 

transcription and user error. A standardized spreadsheet is 

created upon upload (in machine-readable, comma separated 

variable [CSV] format) to the Open Data Kit server. Field 

photos are also transferred with the form, and their file 

names are automatically stored in the spreadsheet. Enketo 

(https://enketo.org/) is another service with similar capabilities 

and a similar user interface that provides support for 

field forms.

Metadata Database

Through this CWRMS effort, a repository for data collection programs and studies throughout the Reserve has been 

created. Members of the PAC have indicated the need for 

metadata and relevant QA/QC data, along with information 

about the intended use of the data by the organization (for 

example, informational only, promoting additional monitoring, 

or influencing regulation), to be maintained and for programs 

to be reviewed by the Reserve Office to ensure future programs document and report the information needed to properly 

catalog their work. As is currently done on an annual basis, 

a request for information on Reserve-related studies can be 

sent to researchers by the Reserve Office. However, this form 

could be provided digitally to allow for easy database entry 

and updating. Additional information from researchers, such 

as a list of procedures and methods used and a data plan to 

be released prior to doing measurements, can be requested in 

order to track what science is being conducted in the Estuary. 

This would be similar to the National Park Service Integrated 

Resource Management Applications forms for research 

conducted within the Office of Parks, Recreation, and Historic 

Preservation property (NPS, n.d.). The Reserve Office would 

also provide guidance for QA/QC documentation and metadata acquisition.

Standardizing the Archival of Data

State and local government agencies with data not housed 

in publicly accessible databases have expressed concern over 

the lack of resources and staff to dedicate to converting paper 

records or older digital records to electronic formats amenable 

to online databases. Deciding on the most compatible and 

transferable database is also a concern. Converting historical 

records and documents to digital format can be time consuming and prone to transcription errors. Assigning the appropriate 

metadata and QA/QC information to historical data can also 

be challenging but provides the context necessary to fully use 

results from past studies and programs.

Both Nassau and Suffolk Counties have historical environmental data that are filed away, with some historical data, 

including most of the data collected in the past 10 years, available upon request in electronic spreadsheets. Preserving historical environmental data originally collected on paper from 

the Reserve in an electronic format would require considerable 

effort and resources. Formatting the data to modern standards 

and migrating it to an open-source database, such as one 

operated by the Federal government, is critical to preserving 

data after a project has ended. In lieu of a publicly accessible 

database hosted by each organization (government, academic, 

or nonprofit), two centralized databases can be utilized for 

this purpose—the Water Quality Exchange (WQX) hosted by 

the National Water Quality Monitoring Council (a collaboration between U.S. Geological Survey and U.S. Environmental 

Protection Agency) and USGS ScienceBase.

As previously noted, there is also a need to account 

for QA/QC documentation whenever possible (or to mark 

a dataset as having “no QA/QC available”). Preservation of 

metadata and QA/QC information associated with a dataset 

allows documentation of changes in methods over the term of 

the project or study, and QC data should be stored as individual records and (or) as part of the metadata associated with 

the environmental dataset, depending on the extent to which 

the QC data are generated. The WQX and ScienceBase offer 

different ways to present QC data. Quality assurance methods can be loaded to the WQX or referenced in ScienceBase 

along with QC data and information. These databases are 

queried by and discoverable through clearinghouses such as 

https://www.data.gov.

The WQX allows for the storage of water-quality and 

biological data in the EPA Storage and Retrieval (STORET) 

database and provides a standardized way in which researchers and other organizations collecting data within the Reserve 

can ensure data are available to the public and preserved in 

perpetuity. STORET can host water-quality, biological, habitat, and indices data and is available at https://www.epa.gov/
Data Gaps and Specific Recommendations 33

waterdata/storage-and-retrieval-and-water-quality-exchange. 

An account is required through the EPA Central Data 

Exchange (https://cdx.epa.gov/), and online tools provided by 

Central Data Exchange allow for data fitted to standardized 

tables to be converted to machine readable files (Extensible 

Markup Language [XML]) for upload to the WQX. Templates 

for organizing data (Microsoft Excel format), as well as for 

identifying methods and some basic metadata associated 

with the data, are available through the instructional website 

(https://www.epa.gov/waterdata/water-quality-exchange-webtemplate-files). A project name and code is required to create a 

node for the agency in the WQX. Once created and verified by 

the EPA, water-quality and ecological data can be transformed 

and uploaded. The data are then accessible through the Water 

Quality Portal, which also queries the USGS National Water 

Information System database, USDA STEWARDS (Sustaining the Earth’s Watersheds—Agricultural Research Database 

System), and others for a comprehensive and dynamic set of 

data. The WQX and STORET are available to any organization wishing to upload data—nongovernmental organizations 

require approval prior to creating a node.

ScienceBase provides flexibility for data storage in that 

the data do not need to be in a specific format and can be 

presented in a variety of file types, from spreadsheets to model 

data outputs. Quality control data can be tabulated or presented in a Portable Document Format (PDF) document and 

uploaded directly to the site. Additionally, metadata files (created using the Online Metadata Editor tool, available through 

the site, and loaded separately from the data being uploaded) 

can include as much information as needed to describe the 

way in which data were collected, analyzed, and processed, 

including the QA/QC. An account and collaborative agreement 

on a USGS research or monitoring project (at the present time) 

is required (USGS, 2017b).

Furthermore, a new service being introduced by the 

USGS soon will allow researchers outside the USGS to use 

crowdsourcing through an open-source program to upload and 

populate databases from digitized field forms as part of the 

Data Rescue Program (Wippich, 2012).

Data Gaps and Specific 

Recommendations

Gaps in the monitoring and management of resources 

ultimately exist because of limited funding. For a lack of data 

in a given waterbody or area to be considered a gap, a need 

must exist for such data to help answer questions related to 

human or ecological health concerns resource managers face. 

The recommendations presented in this section for monitoring water, biological, air, and land resources are summarized 

from stakeholder meetings. In many areas, the data required 

to inform current management plans are not being collected 

at the necessary frequency and (or) spatial resolution because 

the number of variables and capacity to monitor them are cost 

prohibitive. Issues of limited funding can be addressed in 

part by following established guidelines for the collection of 

appropriate data through the coordination of government agencies, academia, and nonprofit and community groups. Some 

examples include intensive localized studies that are transferable to other locations within the Reserve, creating modeling 

and decision support tools, monitoring proxy constituents, and 

citizen science monitoring programs.

In this section, opportunities for synergy among programs 

are also noted to provide information necessary for proposing 

collaboration among governmental, institutional, and community organizations, which can save time and resources while 

generating data. Appendix 1 (tables 1–1 through 1–8) lists 

the monitoring programs and recommended expansions of 

locations and constituents identified in the 2000 Coordinated 

Water Resources Monitoring Strategy, along with updates as to 

which have been fulfilled. By coordinating existing programs 

and capitalizing on the willingness of volunteers and citizen 

scientists to participate in research and monitoring efforts, data 

can be collected in areas where established programs are not 

able to operate, which can help to keep up with the growing 

demand for data in the groundwater and surface waters of the 

Reserve. Examples of data gaps include the need to expand the 

water-quality monitoring network to include additional sites or 

constituents to help identify elevated levels of runoff-related 

contaminants and the need for additional continuous, in situ 

nutrient-monitoring stations to help refine loading budgets and 

models. In addition to the specific monitoring recommendations outlined in this section, several overarching PAC recommendations are summarized to reinforce current efforts and 

introduce new ways to approach monitoring and data management; these new approaches are presented in the section 

“Coordinated Water Resources Monitoring Strategy Website.”

The following sections provide an overview of data gaps 

identified by stakeholders in the areas of water resources, ecology, estuarine dynamics, air resources, and infrastructure. For 

each gap, one or more recommendations for addressing the 

given gap are detailed. A complete listing of data gaps, along 

with associated constituents and management issues from 

table 3 that filling the gap can address, can be found in table 7. 

A “priority” ranking for filling the gaps, based on a survey of 

PAC members, is also presented in table 7.

Water Resources

Presentations by PAC members on water-resource monitoring gaps focused on water-quality and water-quantity constituents specifically needed to inform management decisions.

WATER gap 1.—More real-time water-quality monitoring 

is needed to provide information to decision makers, such as 

why water-quality standards are not being met for a waterbody on the New York State Department of Environmental 

Conservation303(d) list, indications of conditions leading to 

and during fish kills, relative contributions of nutrient loading, 

and potential sources of contamination.
34 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 7. List of gaps in data collection programs identified and prioritized by the Project Advisory Committee for the Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy. [Stakeholder-identified data gaps in environmental monitoring related to water quality are presented along with recommendations compiled from group and individual meetings with the Project Advisory Committee. More details are included in the “Data Gaps and Specific Recommendations” section of this report. Priorities are ranked on a scale from 1–5, with 1 being the most important and 5 being the least important to fill. Constituents needed to fill gaps are abbreviations described in table 1. Capabilities indicate organizations with expertise in filling these gaps. Reserve, South Shore Estuary Reserve; SAV, submerged aquatic vegetation; PPCP, pharmaceutical and personal care product; HAB, harmful algal bloom; lidar, light detection and ranging; USGS, U.S. Geological Survey; SCDHS, Suffolk County Depart- ment of Health Services; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; NYSDEC, New York State Department of Environmental Conservation; CEC, contaminant of emerging concern; NPS, National Park Service; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; TNC, The Nature Conservancy; FWS, U.S. Fish and Wildlife Service; DOS, New York State Department of State; Cornell CE, Cornell Cooperative Extension; GPS, Global Positioning System; ToH,Town of Hempstead; NOAA, National Oceanic and Atmospheric Administration; EPA, U.S. Envi- ronmental Protection Agency] Stakeholder data gaps Gap number Recommendations Constituents needed Management issue addressed Capabilities Pri- ority Water resources Real-time water-quality WATER 1 New real-time water-quality monitoring stations across the Reserve that could be installed or supplement existing USGS, SCDHS, and SoMAS monitors. WT, pH, CHL, DO, NO3, OP MI10, MI14, MI36 SoMAS, TNC, CERCOM, USGS, ToH

2

Real-time streamgages WATER 2 Overlaps in streamgaging by USGS and SCDHS could be eliminated 

and resources shifted to gauge other streams not being assessed to generate a broader dataset.

WL, FLOW -- USGS, SCDHS 4

Routine water-quality data in 

South Oyster Bay

WATER 3 SCDHS and Town of Hempstead should work together with Town of 

Oyster Bay to determine which network will resume sampling.

WT, SAL, pH, DO, 

CHL, TURB, NUT, SS

MI24 ToH, SCDHS, 

NYSDEC

4

Continuous nitrate data WATER 4 Work with agencies and academics to identify sites where nitrate data 

are needed, and fund the operation and maintenance of available sensors.

NO3 MI38 SoMAS 3

Continuous water temperature and 

dissolved oxygen depth profiles

WATER 5 Expand ongoing USGS, TNC, and SoMAS profiling currently in Nicoll 

Bay and Great South Bay throughout the bays, mouths of tributaries, and at inlets to assess vegetation and fish survey data.

DO, WT, SAL MI18, MI36 USGS, TNC, 

SoMAS

3

Loading of pesticides, herbicides, 

and PPCPs to the bays

WATER 6 Focused studies by universities and Federal partners should seek to correlate nitrogen with pesticide and PPCP occurrences and concentrations in groundwater and surface waters. CEC, NO3, GWL MI13 SoMAS, USGS 1

Sources and relative contributions 

of pathogens that are loading to bays and tributaries

WATER 7 Support current action plans for monitoring receiving waters of stormwater and wastewater outfalls; apply advanced models to help predict 

bacteria at beaches and shellfish areas; microbial source tracking studies should be coordinated; Canadian geese monitoring should be included in shellfish programs.

PATH, SHELLS, 

WILD

MI21, MI27, 

MI32

NYSDEC, SoMAS, 

USGS

3

Changes in water quality resulting from the construction of 

wastewater treatment plants and remediation

WATER 8 Coordination among monitoring agencies and planning departments 

should occur in the early stages of development to allow for waterquality monitoring resources to be identified in the area or installed if needed to create a baseline dataset.

SAL, WT, pH, DO, 

TURB, NO3, CHL, fDOM

MI29 Town of Brookhaven, Suffolk 

County, academics, USGS

4

Water-quality data on the ocean 

side

WATER 9 Water quality buoys, similar to those deployed by SoMAS, could be 

used near inlets on the ocean side of the barrier islands.

WT, AT, pH, 

SAL, WVH, WEATHER

-- SoMAS, NOAA 5
Data Gaps and Specific Recommendations 35

Table 7. List of gaps in data collection programs identified and prioritized by the Project Advisory Committee for the Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy.—Continued[Stakeholder-identified data gaps in environmental monitoring related to water quality are presented along with recommendations compiled from group and individual meetings with the Project Advisory Committee. More details are included in the “Data Gaps and Specific Recommendations” section of this report. Priorities are ranked on a scale from 1–5, with 1 being the most important and 5 being the least important to fill. Constituents needed to fill gaps are abbreviations described in table 1. Capabilities indicate organizations with expertise in filling these gaps. Reserve, South Shore Estuary Reserve; SAV, submerged aquatic vegetation; PPCP, pharmaceutical and personal care product; HAB, harmful algal bloom; lidar, light detection and ranging; USGS, U.S. Geological Survey; SCDHS, Suffolk County Department of Health Services; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; NYSDEC, New York State Department of Environmental Conservation; CEC, contaminant of emerging concern; NPS, National Park Service; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; TNC, The Nature Conservancy; FWS, U.S. Fish and Wildlife Service; DOS, New York State Department of State; Cornell CE, Cornell Cooperative Extension; GPS, Global Positioning System; ToH,Town of Hempstead; NOAA, National Oceanic and Atmospheric Administration; EPA, U.S. Environmental Protection Agency]

Stakeholder data gaps Gap number Recommendations Constituents needed Management issue addressed Capabilities Pri- ority

Water resources—Continued

Loading of microplastics to the 

water column and bed sediment

WATER 10 Grab samples of water during base-flow and stormflow conditions would 

help quantify and classify microplastic contamination in the bays and tributaries.

MP MI17 USGS, NOAA, EPA, 

academics

2

High-resolution groundwater 

model for contaminant loading

WATER 11 Define groundwater loading on local levels based on groundwater contributing areas and travel times and couple with loading calculations. GWL, NUT MI26 USGS, consultants 2

Ecological Resources

Impacts to ecosystems resulting from the loading of PPCP, 

pesticides, and endocrine disruptors.

ECOLOGY 1 More research is needed to study the effects of concentrations of CECs. CEC, SHELLT MI10 NYSDEC, New 

York Sea Grant, academics

2

Marine resources data ECOLOGY 2 Collection of fish surveys and biological data can be coordinated with 

across organizations interested in supplementing biological or waterquality monitoring.

SHELLS, AT, WT, 

DEPTH, SAL, SR, SAV

MI8, MI21, 

MI23, MI37

NPS, NYSDEC, academics, towns 3

Aerial photographs and mapping 

surveys for SAV

ECOLOGY 3 Drones (aerial and submersibles) could be used for bathymetry and 

submerged aquatic vegetation purposes.

PHOTO, WT, SAV MI35 TNC, USGS, 

NYSDEC, SoMAS

2

Biological and chemical factors 

leading to brown tide and other HAB species

ECOLOGY 4 Additional support needed for water-quality monitoring (physical parameters, nutrients, water clarity, fertilizers and pesticides) and sampling by the Suffolk County, Town of Hempstead, and other Federal 

and local partners, which could be synchronized with ongoing HAB sampling and research to provide additional data for interpretation.

WT, SAL, pH, DO, 

CHL, TURB, NUT, PAR, NA/HAB

MI21, MI37 SoMAS, NYSDEC, 

SCDHS, ToH, USGS

1

Water-quality to support fish 

habitat restoration

ECOLOGY 5 SCDHS monitoring could be coordinated with Cornell Cooperative Extension to get depth profiles more frequently, and Cornell Cooperative 

Extension could work with SoMAS and TNC to deploy additional buoys and continuous profilers in areas of restoration.

WT, SAL, pH, DO, 

CHL, TURB, NO3, PAR, SS

MI21, MI22 SCDHS, Cornell CE, 

TNC, NYSDEC

1

Horseshoe crab data and coordination ECOLOGY 6 Agreement on standardized methods for horseshoe crab survey and tissue collection is needed and should be sought by DEC, TNC, NPS, 

local universities.

WILD, HSC MI31 TNC, NYSDEC, 

NPS, Molloy College

3
36 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 7. List of gaps in data collection programs identified and prioritized by the Project Advisory Committee for the Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy.—Continued [Stakeholder-identified data gaps in environmental monitoring related to water quality are presented along with recommendations compiled from group and individual meetings with the Project Advisory Committee. More details are included in the “Data Gaps and Specific Recommendations” section of this report. Priorities are ranked on a scale from 1–5, with 1 being the most important and 5 being the least important to fill. Constituents needed to fill gaps are abbreviations described in table 1. Capabilities indicate organizations with expertise in filling these gaps. Reserve, South Shore Estuary Reserve; SAV, submerged aquatic vegetation; PPCP, pharmaceutical and personal care product; HAB, harmful algal bloom; lidar, light detection and ranging; USGS, U.S. Geological Survey; SCDHS, Suffolk County Depart- ment of Health Services; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; NYSDEC, New York State Department of Environmental Conservation; CEC, contaminant of emerging concern; NPS, National Park Service; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; TNC, The Nature Conservancy; FWS, U.S. Fish and Wildlife Service; DOS, New York State Department of State; Cornell CE, Cornell Cooperative Extension; GPS, Global Positioning System; ToH,Town of Hempstead; NOAA, National Oceanic and Atmospheric Administration; EPA, U.S. Envi- ronmental Protection Agency] Stakeholder data gaps Gap number Recommendations Constituents needed Management issue addressed Capabilities Pri- ority Estuarine Dynamics Data to understand impacts of sea-level rise on wetlands and marsh islands ESTUARY 1 Correlate high-resolution satellite and aerial photography and infrastruc- ture (land use) data, wetlands and riparian zone areas, and water-level data collected throughout the Reserve on an annual basis to document changes. TOPO, SET, IN- VFL, VEG MI19, MI25, MI28, MI33, MI34 NOAA, USGS, TNC, FWS

2

A comprehensive assessment of 

bed-sediment quality across the Reserve

ESTUARY 2 Research conducted at SoMAS and other organizations for wastewater 

tracers, particle size, and organic nitrogen and carbon in Hempstead Bay and could be expanded both in space and constituent type.

PPOL, CEC, 

PART, MP, SR

MI16, MI17 SoMAS 3

Post-Hurricane Sandy geomorphology, especially bayside of 

the barrier islands

ESTUARY 3 Apply current data and models to better understand bayside and ocean 

side geomorphology and sediment transport.

BATHY, SR MI34 SoMAS, USGS 3

Sediment flux from tributaries to 

bays

ESTUARY 4 Sediment transport, velocity of currents, and geomorphic profile should 

be conducted.

BATHY, SR, 

WVE, WVH

MI19 Lamont-Doherty 

Earth Observatory—Columbia University

3

Marsh area and sediment transport 

data to establish long-term trends

ESTUARY 5 Decadal-scale updates to these surveys with the most up-to-date remote 

sensing technology would allow for consistent monitoring of progress towards addressing the loss of marsh lands and should incorporate updated land-use data and trends in water-quality data to inform threats to restoration effort.

PHOTO, TOPO, 

WVE, SET, SR

MI19, MI34 NPS, USGS, 

NYSDEC, academics, Shinnecock Tribal Nation, SCDHS, towns, TNC, Cornell CE

2

Ecological and physical impacts 

of the breach at Old Inlet

ESTUARY 6 Continuous water-level and water-quality monitoring at the inlet via a 

buoy that measures turbidity, water temperature, salinity, and fluorescence is needed, as well as an assessment of phytoplankton blooms, including brown tide, and an inventory of finfish and macroinvertebrates.

WL, WT, SAL, 

CHL, WILD, MACRO, NA/HAB

-- SoMAS, CERCOM 2

Sediment- and water-quality data 

to support study on whether marshes in the Reserve act as a nitrogen source or sink

ESTUARY 7 Detailed nutrient and microbial analysis of sediment and pore water 

under laboratory conditions and in situ could be coordinated to better understand the fate of nitrogen entering marshes.

NUT, ISOT, pH, 

DO, WT, ORP, TOC, TON

MI19 SoMAS, SCDHS, 

ToH, Suffolk County Vector Control

3
Data Gaps and Specific Recommendations 37

Table 7. List of gaps in data collection programs identified and prioritized by the Project Advisory Committee for the Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy.—Continued[Stakeholder-identified data gaps in environmental monitoring related to water quality are presented along with recommendations compiled from group and individual meetings with the Project Advisory Committee. More details are included in the “Data Gaps and Specific Recommendations” section of this report. Priorities are ranked on a scale from 1–5, with 1 being the most important and 5 being the least important to fill. Constituents needed to fill gaps are abbreviations described in table 1. Capabilities indicate organizations with expertise in filling these gaps. Reserve, South Shore Estuary Reserve; SAV, submerged aquatic vegetation; PPCP, pharmaceutical and personal care product; HAB, harmful algal bloom; lidar, light detection and ranging; USGS, U.S. Geological Survey; SCDHS, Suffolk County Department of Health Services; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; NYSDEC, New York State Department of Environmental Conservation; CEC, contaminant of emerging concern; NPS, National Park Service; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; TNC, The Nature Conservancy; FWS, U.S. Fish and Wildlife Service; DOS, New York State Department of State; Cornell CE, Cornell Cooperative Extension; GPS, Global Positioning System; ToH,Town of Hempstead; NOAA, National Oceanic and Atmospheric Administration; EPA, U.S. Environmental Protection Agency]

Stakeholder data gaps Gap number Recommendations Constituents needed Management issue addressed Capabilities Pri- ority

Atmospheric Resources

Air resources should be looked at 

more closely for pollutant levels and the extent of deposition to the waters of the Reserve

AIR 1 The NYSDEC air-quality sampling network to include sites along the 

South Shore.

WEATHER, AQ -- EPA, counties, 

academics, USGS, NWS

3

Infrastructure and Land Use

High-resolution mapping of all 

storm drains, sewer lines, storm sewer lines, and outfalls, as well as cesspool/septic density in unsewered areas

INFRASTRUCTURE 1 Detailed coverages of sewered areas exist through Suffolk County Planning; though indicating which homes are not hooked up in both Counties are needed. LU, IMPCOV, SDO, STP, TOPO, INUN, 

PHOTO

MI29, MI30 Cornell CE, Suffolk 

County, Nassau County

1

Detailed and current mapping of 

zoning developments throughout the Reserve

INFRASTRUCTURE 2 A revised version of the current land use maps is needed and should be coordinated between Nassau and Suffolk Counties. LU -- Suffolk County, Nassau County 4
38 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

Recommendations to address WATER gap 1.—Overlaps 

in water-quality monitoring by the U.S. Geological Survey 

and Suffolk County Department of Health Services (SCDHS) 

could be eliminated and resources shifted to monitoring other 

streams not being assessed to generate a broader dataset. New 

real-time water-quality monitoring stations across the Reserve 

that could be installed or supplement existing USGS, SCDHS, 

and Stony Brook University School of Marine and Atmospheric Sciences monitors include stations at Shinnecock Bay, 

Moriches Bay, Forge River, Patchogue River, Carmans River, 

Nicoll Bay, Connetquot River, Carlls River, Lindenhurst (the 

current [2017] USGS station could be upgraded), South Oyster 

Bay, Massapequa Creek, Meadowbrook Creek, and East and 

Middle Bays between Point Lookout and Jones Inlet. An additional station should also be added in Great South Bay (a site 

on Great South Bay Bridge should be considered). Tributary 

sites should include stage and flow; bay sites would include 

water-level elevation. The following in situ water-quality 

constituents are needed: water temperature, pH, total algae 

(phycoerythrin) and chlorophyll a, dissolved oxygen, nitrate, 

and orthophosphate.

WATER gap 2.—More real-time streamgages are needed 

in streams prone to flooding to inform resource managers of 

runoff volumes for loading calculations and to notify emergency responders of potential flooding events.

Recommendations to address WATER gap 2.—Overlaps 

in streamgaging and water-quality testing by the USGS and 

SCDHS could be eliminated, and resources could be shifted 

to gage other streams not being assessed to generate a broader 

dataset. Streams with fish runs or dam modification should be 

prioritized. County data needs to be made available online via 

the county portal or data.gov.

WATER gap 3.—Routine water-quality monitoring in 

South Oyster Bay has not been conducted in over 10 years and 

should be reinstated.

Recommendations to address WATER gap 3.—SCDHS 

and the Town of Hempstead should work together with the 

Town of Oyster Bay to determine which network will resume 

sampling of at least the three original sites in South Oyster 

Bay for constituents consistent with current Great South Bay 

and Hempstead Bay monitoring.

WATER gap 4.—More continuous nitrate data are needed 

to understand how changes in water temperature affect nutrient concentrations.

Recommendations to address WATER gap 4.—Agencies 

and academics should collectively identify sites where nitrate 

data are needed and to fund the operation and maintenance of 

available sensors.

WATER gap 5.—There is a need for continuous water 

temperature and dissolved oxygen depth profiles in bays 

throughout the Reserve in order to relate diurnal and seasonal 

fluxes to the health and loss of submerged aquatic vegetation 

(SAV) (such as eelgrass), flushing dynamics, and shellfish 

health.

Recommendations to address WATER gap 5.—Dissolved 

oxygen profiles and bottom temperature monitoring is ongoing 

since 2015 in Nicoll Bay and Great South Bay as part of an 

effort by the USGS and The Nature Conservancy to assess 

the areas of hypoxia of Great South Bay. SoMAS has also 

deployed the same dissolved oxygen sensors at these sites for 

a different study. This type of monitoring could be expanded 

throughout the bays, mouths of tributaries, and inlets and 

could be used to assess vegetation and fish survey data.

WATER gap 6.—Insufficient data are available on the 

loading of pesticides, herbicides, and pharmaceuticals and personal care products (PPCPs) to the bays, marshes, and ecosystems of the Reserve. Similarly, effects on ecosystems resulting 

from the loading of these anthropogenic compounds, such as 

endocrine disruption in finfish, are not well understood.

Recommendations to address WATER gap 6.—Focused 

studies by universities and Federal partners should seek to 

correlate nitrogen with pesticide and PPCP occurrences and 

concentrations in groundwater and surface waters. To develop 

correlations, localized and regional studies are needed that 

monitor nutrients in groundwater and tributaries and the concentrations of PPCPs and endocrine-disrupting compounds. 

Such studies are especially needed in shallow groundwater 

with short traveltimes to the bays and where sewage treatment 

plants discharge.

WATER gap 7.—Sources and relative contributions of 

pathogens that are loading to bays and tributaries throughout 

the Reserve need to be better defined; pathogen sources must 

be differentiated between wildlife and human.

Recommendations to address WATER gap 7.—State or 

Federal funding should be sought to support current action 

plans for monitoring receiving waters of stormwater and 

wastewater outfalls discharging to the Reserve.

Additional recommendations to address WATER gap 7.—

Apply advanced models, such as USGS Nowcast, to help 

predict bacteria at beaches and shellfish areas given a set of 

constituents (that are collected in real time) by using data collected by Suffolk and Nassau Counties, the NYSDEC, towns, 

and SoMAS. The NYSDEC has modeled some effects but 

does not have field data to corroborate models.

Additional recommendations to address WATER gap 7.—

Microbial source tracking studies should be coordinated. For 

example, coordination could include looking at wildlife surveys, DNA/RNA sequencing, and polymerase chain reaction 

(PCR) methods. 

Additional recommendations to address WATER gap 7.—

Canadian geese monitoring should be included in shellfish 

programs to determine impacts (correlate geese survey [spatial 

and temporal] data with closures of areas to shellfishing and 

pathogen monitoring data).

WATER gap 8.—There is a need to track changes in 

water quality resulting from the construction of wastewater 

treatment plants (for example, in Mastic/Shirley), redevelopment of existing wastewater infrastructure (for example, 

diverting effluent from Bay Park Sewage Treatment Plant), 

and remediation (for example, any remediation of Forge River 

bed sediment).
Data Gaps and Specific Recommendations 39

Recommendations to address WATER gap 8.—Coordination among monitoring agencies and planning departments 

should occur in the early stages of development to allow for 

water-quality monitoring resources to be identified in the area 

or installed, if needed, to create a baseline dataset. For Mastic/

Shirley, the Town of Brookhaven along with Suffolk County, 

university partners, and the USGS should coordinate to install 

and maintain a continuous water-quality observatory station in 

western Moriches Bay near the mouth of the Forge River. For 

Bay Park, coordination between the Town of Hempstead, Nassau County, the NYSDEC, university partners, and the USGS 

is needed to maintain existing and ensure proper temporal and 

spatial monitoring.

WATER gap 9.—Water-quality data are lacking on the 

ocean side to understand changes within the bay relating to 

ocean acidification and rising global temperature.

Recommendations to address WATER gap 9.—Waterquality buoys, similar to those deployed by SoMAS, could be 

used to monitor pH, water and air temperature, salinity, wave 

height, and wind at locations near inlets (ocean side).

WATER gap 10.—An understanding of the concentration 

and loading of microplastics to the water column and bed sediment in the bays is needed.

Recommendations to address WATER gap 10.—Grab 

samples of water during base-flow and stormflow conditions 

would help quantify and classify microplastic contamination 

in the bays and tributaries. Bed sediment grab samples and 

cores would provide rates of loading to the benthic environment. This effort could be conducted locally by universities 

in cooperation with the National Oceanic and Atmospheric 

Administration (NOAA), the U.S. Environmental Protection 

Agency, and other Federal agencies.

WATER gap 11.—A high-resolution groundwater model 

for contaminant loading is needed in coastal areas where 

changes in wastewater infrastructure are being considered.

Recommendations to address WATER gap 11.—Define 

groundwater loading on local levels based on groundwater 

contributing areas and traveltimes currently being modeled by the USGS and coupled with loading calculations 

being developed under the Long Island Nitrogen Action Plan 

(LINAP). Use the Watershed MVP mapper program and create 

a decision support tool that also dynamically links with current 

monitoring resources.

Ecological Resources

Presentations by PAC members on gaps in ecological 

resources focused on assessments that are needed of the water 

quality or biology within the Reserve.

ECOLOGY gap 1.—Effects on ecosystems resulting 

from the loading of pharmaceuticals, pesticides, and endocrine 

disruption are not well understood.

Recommendations to address ECOLOGY gap 1.—More 

research is needed to study the effects of concentrations of 

contaminants of emerging concern found in the waters and 

bed sediment of the Reserve on finfish and shellfish pathology. 

This includes studies that assess seasonal effects and complex 

mixtures.

ECOLOGY gap 2.—More marine resources data are 

needed, including data on the population and health of plankton, finfish (such as juvenile eels) and crustaceans. Limited 

fish seining data are available.

Recommendations to address ECOLOGY gap 2.—NPS 

conducts only some fish surveys and collects only some 

biological data through research agreements. These efforts can 

be coordinated with other organizations interested in supplementing biological or water-quality monitoring. This could be 

done through notifications from NPS to the Reserve Office, 

which would then reach out to other groups. For example, a 

survey of shellfish in the Reserve could be leveraged to collect the following constituents along with count (per standard survey method of the Reserve waters): air temperature, 

water temperature, water depth, salinity, sediment type, and 

amount of eelgrass. The following list of tributaries should be 

surveyed for finfish in marine and freshwater extents: Massapequa Creek, Carlls River, Connetquot River, Carmans River, 

and Swan River. Studies by SoMAS should be expanded to 

more fully investigate the biology and chemistry of harmful 

algal blooms (HABs) and use recommended monitoring data 

in interpretation.

ECOLOGY gap 3.—Aerial photographs and mapping 

surveys for SAVs, similar to those done in the Peconic Estuary 

and Chesapeake Bay, are in need of updating because eelgrass 

are still disappearing (although some are reappearing or being 

replanted around the breach).

Recommendations to address ECOLOGY gap 3.—Drones 

(aerial and submersibles) could be used for bathymetry and 

SAV purposes. SoMAS, USGS, CERCOM, and The Nature 

Conservancy (TNC) programs can be expanded to increase the 

number of fixed stations and buoys to provide greater realtime data coverage. Continuous water temperature profiling 

and bottom temperature measurements throughout the estuary 

can relate to SAV health (including loss of eelgrass), as well as 

other ecological indicators, and flushing dynamics and thus are 

also needed.

ECOLOGY gap 4.—More research is needed to understand the biological and chemical factors leading to brown tide 

and other HAB species.

Recommendations to address ECOLOGY gap 4.—Currently, SoMAS research is evaluating the increasing frequency 

at which HABs are occurring throughout the Reserve (and in 

particular, Great South Bay and the eastern bays). Along with 

additional support for SoMAS and other universities in the 

area, water-quality monitoring (physical constituents, nutrients, water clarity, fertilizers, and pesticides) and sampling by 

the Suffolk County, the Town of Hempstead, and the USGS 

could be synchronized with HAB sampling to provide additional data for interpretation. Monitoring strategies presented 

in the recently released Suffolk County Harmful Algae Bloom 

Action Plan (Wise, 2017) should be considered as action items 
40 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

are implemented to help reduce the number of nuisance and 

harmful blooms that occur in the waters around Long Island.

ECOLOGY gap 5.—Restoration of fish habitat requires 

consistent monitoring of temperature (throughout the water 

column), light availability, turbidity, dissolved oxygen, and 

salinity, and this monitoring is not currently being conducted.

Recommendations to address ECOLOGY gap 5.—The 

SCDHS Office of Ecology monitors all bays of the Reserve in 

Suffolk County and could be coordinated with Cornell Cooperative Extension to collect depth profiles more frequently. 

Furthermore, Cornell Cooperative Extension could work with 

SoMAS and TNC to deploy additional buoys and continuous profilers in areas of restoration. The USGS is testing an 

autonomous underwater vehicle that can map large portions of 

the bay floors with high-resolution bathymetry and also record 

temperature, light penetration, and other water-quality constituents. Public notice and outreach regarding the restoration and 

how it benefits habitat to improve water quality and fishing in 

the bay should continue on a large scale to build support in the 

communities, and this outreach should be correlated with the 

outreach for shellfish-bed and habitat monitoring. The Peconic 

Estuary Program and Chesapeake Bay eelgrass restoration 

and monitoring efforts have proven successful (Pickerell and 

Schott, 2014).

ECOLOGY gap 6.—Horseshoe crab data are collected by 

several agencies and universities but not coordinated; data are 

missing for some regions of the Reserve.

Recommendations to address ECOLOGY gap 6—Agreement on standardized methods for horseshoe crab survey and 

tissue collection should be sought by the NYSDEC, TNC, 

NPS, Cornell Cooperative Extension, and Molloy College 

in order to allow data from these organizations to be comparable and used for making management decisions. Coordination among the same groups would allow for sites not being 

assessed to be visited and improve the overall coverage and 

density of the horseshoe crab network (some sites within the 

programs overlap and would provide data quality checks in 

some cases). Quality assurance can be evaluated to ensure 

compatibility among programs. A single database for these 

data would be beneficial.

Estuarine Dynamics

Presentations by PAC members on estuarine resource 

gaps focused on hydrodynamics, bathymetry, and sediment 

flux within the Reserve.

ESTUARY gap 1.—More data are needed to understand effects of sea-level rise on wetlands and marsh islands, 

updated mapping of Spartina and Phragmites is needed for 

the entire Reserve, and coordinating aerial light detection and 

ranging (lidar) surveys with SET site data is needed (and may 

require additional SET sites for better spatial coverage).

Recommendations to address ESTUARY gap 1—Correlate high-resolution satellite and aerial photography and infrastructure (land-use) data, wetlands and riparian zone areas, and 

water-level data collected throughout the Reserve on an annual 

basis to document changes. Continued collection of aerial 

vegetation data by the U.S. Fish and Wildlife Service (FWS) 

would support wetland loss studies. Coordinate a study with 

high-frequency wave sensors along vulnerable wetlands to 

determine the extent of wave energy and its effects on erosion.

Additional recommendations to address ESTUARY 

gap 1.—Citizen science can be used to survey and groundtruth Spartina and Phragmites in wetlands and correlate resulting data with changes in land use and water chemistry. Coordinate the SET installation and monitoring (including reporting, 

when-measured, and unit specifications) effort among various 

groups; consider additional SET marker horizons. A coordinated database of SET data would be useful.

ESTUARY gap 2.—A comprehensive assessment of bedsediment quality across the Reserve is needed because it can 

reveal information about denitrification in the hyporheic zone 

and bay bottom, sediment transport, and contaminant loading 

and persistence.

Recommendations to address ESTUARY gap 2.—The 

sediment-quality analyses outlined by Woods Hole Group 

(2010) suggest that bed-sediment-quality data throughout the 

Reserve are lacking. Research conducted at SoMAS looks 

at novel sewage and wastewater tracers, particle size, and 

organic nitrogen and carbon in Hempstead Bay and could be 

expanded both in space (entire key locations in the Reserve, 

including bays and tributaries) and constituent type (for 

example, total inorganic and organic nitrogen and carbon, metals, and radioisotopes for age-dating).

Additional recommendations to address ESTUARY 

gap 2.—A transect of sediment-quality data across the Great 

South Bay in areas where chronic low dissolved oxygen is 

observed would be useful. Coordination among Nassau and 

Suffolk Counties, the Town of Hempstead, the NYSDEC 

and the New York State Department of State (NYSDOS), the 

USGS, NOAA (Mussel Watch), the EPA (National Coastal 

Condition Assessment program), and SoMAS would be 

needed to ensure resources and capacities (including split 

samples when program sample efforts overlap) are in place 

and management issues discussed prior to establishing a network and sampling.

ESTUARY gap 3.—A better understanding of post-Hurricane Sandy geomorphology of shorelines is needed, especially 

bayside of the barrier islands, through collection of more data 

for bathymetry and channel depth, including more nearshore 

and shallow-water work to survey the bay bottom.

Recommendations to address ESTUARY gap 3.—Apply 

current data and models to better understand bayside and 

oceanside geomorphology and sediment transport.

Additional recommendations to address ESTUARY 

gap 3.—High-resolution bathymetry should be conducted (by 

boat or autonomous underwater vehicle) to create a baseline 

for the Reserve bottom ahead of the next major coastal storm 

that redistributes large volumes of sediment. This could be 

conducted simultaneously with SAV and shellfish surveys 

(either hyperspectral or visual) and updated after major 
Data Gaps and Specific Recommendations 41

dredging operations or coastal storms that cause substantial 

sediment redistribution.

ESTUARY gap 4.—A better understanding is needed of 

sediment flux from tributaries to bays, sediment deposition 

and transport across the bay bottom, and how distribution 

relates to legacy contamination.

Recommendations to address ESTUARY gap 4.—Sediment transport, current-velocity, and geomorphic profile data 

should be collected in the Carlls River and Carmans River 

watersheds initially and then in other larger tributaries as 

needed.

ESTUARY gap 5.—Marsh area and sediment transport data should be collected on a regular basis to establish 

long-term trends in changes in geomorphology and wetland 

loss (for example, marsh conversion from high marsh to low 

marsh is not keeping up with changes in water levels in the 

bays). Automated measuring of sediment flux through inlets 

and tracking of sea-level rise would inform an understanding 

of net transport to or from the estuary. The extent to which 

boats and other watercraft affect marsh islands and shoreline 

resiliency is not well known. Correlating storm effects with 

the root depth and health of vegetation is important. A loss of 

native grasses such as Spartina resulting in decreasing arthropods (particularly in the Bay Park area) has been observed.

Recommendations to address ESTUARY gap 5.—Comparisons of marsh areas and grasses (for example, Spartina

and Phragmites) that were conducted for the New England 

Interstate Water Pollution Control Commission by using 

aerial surveys from the 1974 and the 2005 and 2008 fly-overs 

(Cameron Engineering & Associates, LLP., 2015) accounted 

for roughly 11 percent of marsh loss in the Reserve. Decadalscale updates to these surveys with the most up-to-date remote 

sensing technology will allow for consistent monitoring of 

progress towards addressing the loss of marshlands (NYSDEC, n.d.[d]) and should be incorporated into updated landuse data and trends in water-quality data to provide updates on 

the restoration effort.

Additional SETs may be needed since marshes are being 

affected by rising sea level. Coordinate the SET installation 

and monitoring (including reporting, when-measured, and unit 

specifications) among the NPS, TNC, the Shinnecock Tribe, 

and the USGS and consider additional SETs at the following stations to supplement the current network: select marsh 

islands of Middle Bay and East Bay, barrier island marsh 

of South Oyster Bay, marsh island adjacent to Fire Island 

Inlet, and marsh in the southern part of the Shinnecock Tribal 

Lands peninsula.

High-frequency wave sensors could be deployed along 

vulnerable wetlands to determine the extent of wave energy 

and its effects on erosion.

ESTUARY gap 6.—A better understanding of the ecological and physical (such as flooding, flushing, and inundation) 

effects of the breach at Old Inlet is needed.

Recommendations to address ESTUARY gap 6.—Continuous water-level and water-quality monitoring at the inlet via 

a buoy that measures turbidity, water temperature, salinity, and 

fluorescence is needed to support the existing LIShore Bellport 

Station (Bellport Bay; located across the breach).

Additional recommendations to address ESTUARY 

gap 6.—A focused evaluation of ecological resources in the 

bays and tributaries adjacent to the breach could be conducted 

from data from the estuary-wide studies of algae, finfish, and 

macroinvertebrates.

ESTUARY gap 7.—More studies are needed to understand whether marshes in the Reserve act as a nitrogen source 

or sink.

Recommendations to address ESTUARY gap 7.—Detailed 

nutrient and microbial analysis of sediment and pore water 

under laboratory conditions and in situ could be coordinated 

between SoMAS, the Town of Hempstead, the SCDHS, and 

Suffolk County Vector Control to better understand the fate of 

nitrogen entering marshes through groundwater seepage, from 

the water column, and from atmospheric deposition.

Atmospheric Resources

Presentations by PAC members on the gap in atmospheric 

resources focused on understanding how air quality can affect 

the water quality and ecology of the Reserve.

AIR gap 1.—Air resources should be looked at more 

closely, including levels of nitrogen dioxide and other pollutants (for example, ozone, mercury, and particulates) and the 

extent of deposition to the waters of the Reserve.

Recommendations to address AIR gap 1.—The NYSDEC 

should expand the ambient air monitoring network to include 

additional sites along the south shore.

Additional recommendations to address AIR gap 1.—A 

station similar to the National Atmospheric Deposition Program’s wet weather station in Southold should be established 

somewhere mid-island and monitor for dry- and wet-weather 

deposition and concentration of contaminants, including acid 

rain (pH), ozone, and nitrogen dioxide.

Infrastructure and Land Use

Specific monitoring of infrastructure relative to water and 

ecological resources was presented by members of the PAC as 

a gap in two ways.

INFRASTRUCTURE gap 1.—High-resolution mapping 

of all storm drains, sewer lines, storm sewer lines, and outfalls, 

as well as cesspool and septic density in unsewered areas, 

is needed throughout the Reserve; a complete dataset could, 

among other uses, provide inputs for source tracking models.

Recommendations to address INFRASTRUCTURE 

gap 1.—The 2008 Stormwater Infrastructure Mapping Inventory and Assessment (New York State Department of State 

Office of Planning and Development South Shore Estuary 

Reserve Council, 2008) identified the extent to which outfalls 

and storm sewers were documented by government agencies 

within the Reserve. The report found varying degrees of accuracy, detail, and completeness and made recommendations 
42 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

for filling the gaps among the 39 municipalities responsible 

for handling stormwater. These recommendations should 

be followed, with data being ultimately housed on the New 

York State Geographic Information Systems Clearinghouse, 

which exists to host all relevant GIS data within the State. 

Detailed coverages of sewered areas exist through the Suffolk 

County Division of Planning and Environment; identification 

of homes that are not hooked up in both Counties would be 

helpful. Additional mapping efforts should provide layers for 

the Reserve water-quality mapper. Continue to support Cornell 

Cooperative Extension mapping effort, and determine what 

towns and counties (some involved in localized work done as 

part of the Comprehensive Management Plan development 

for select watersheds) still need their stormwater infrastructure mapped (the mapping would be done by citizen scientists 

provided with standardized GPS units and basic training [by 

boat and land]). The Reserve Office could help facilitate the 

move to a single database for infrastructure projects (including 

best management practices [BMPs] and green infrastructure) 

within the Reserve, and the database could include project 

specifics along with any relevant water-quality monitoring 

data from before and after the project and associated with 

affected waters.

INFRASTRUCTURE gap 2.—More detailed and current 

mapping of zoning developments throughout the Reserve is 

needed. Land-use maps were updated every 5 years (latest version released in 2012); updates are no longer done because of 

high cost and loss of staffing.

Recommendations to address INFRASTRUCTURE 

gap 2.—Revised versions of the current land-use maps are 

needed and should be coordinated between Nassau and Suffolk Counties and possibly funded through a State grant. These 

land-use data will be used for groundwater and watershed 

modeling and decision tools. Attributes for digital GIS maps 

should include wastewater management (specifically cesspool, 

septic, sewered, and stormwater) and water supply.

General and Coordination 

Recommendations From the Project 

Advisory Committee

A number of management plans have been developed for 

groundwater and surface waters that include some or all of 

the Reserve (table 2; appendix 3). Thirty of these plans have 

been funded by the New York State Department of State since 

2000 to study the ecological health and potential for improvements in the Reserve. These plans outline different issues 

facing the Reserve and propose which organization is most 

capable to address the issue and how it could do so. The plans 

tend to have similar formats, with only subtle differences, for 

describing issues that actually relate to the entire Reserve. 

Members of the Project Advisory Committee have emphasized the importance of following through on implementing 

recommendations in comprehensive management plans in a 

coordinated and mutually beneficial manner to maximize efficiency among the organizations performing the tasks.

This section summarizes recommendations of the PAC 

and is intended to help synchronize water-quality and ecological monitoring throughout the Reserve in order to meet 

management objectives and address issues. Recommendations presented here are a compilation of comments recorded 

at the PAC meetings and workshop, as well as meetings with 

researchers and representatives of organizations with a vested 

interest in the Reserve. These recommendations are programmatic and overarching rather than specific to constituent or 

monitoring type, and generally they address the management 

issues raised by stakeholders and summarized in the introduction and in table 3.

General Recommendations of the Project 

Advisory Committee

Although addressing gaps in monitoring and data collection throughout the Reserve (see the section “Data Gaps and 

Specific Recommendations”) can be a relatively straightforward effort, coordinating efforts around projects that focus 

on resources and resiliency, developing and utilizing existing 

tools for assessing water quality and ecological health, and 

engaging community groups to help improve awareness of 

the resources is not always easy. Management issues outlined 

in table 3 often overlap spatially and may require similar 

data and quality assurances to be addressed. The PAC has 

made the following general recommendations that can help 

coordinate the collection and use of data from current and 

proposed programs:

1. Standardization of data and metadata

2. Expansion and enhancement of real-time water-quality 

monitoring

3. Coordination with citizen science organizations

4. Updating of municipal-land-use maps

5. Expansion of remote sensing technology

6. Use of advanced hydrodynamic models

7. Use of a decision support tool for understanding changes 

to loading of nutrients

8. Implementation of a network of rapid-deployment waterquality monitors

9. Coordination of groundwater-quality sampling

10. Monitoring of preserved lands through expansion of the 

Community Preservation Fund

11. Investigation of effects of moving the Bay Park Sewage 

Treatment Plant outfall
General and Coordination Recommendations From the Project Advisory Committee 43

12. Enhanced documentation of long-term water-quality 

changes

Details for each recommendation follow:

1. Standardizing data across monitoring programs and 

studies would maximize data usage and availability for 

model input (that is, combining south shore environmental monitoring data with those from the Long Island 

Sound Study [LISS] and the Peconic Estuary Program 

[PEP], including documentation of standardized procedures and analytic results, and storing the data in a centralized location). This includes data that are collected 

outside the Reserve but are relevant to water quality and 

the ecological health of Long Island. Specific examples 

of data standardization include the following:

A. Estuarine water-quality data should be analyzed and 

stored by following consistent methods agreed upon 

by all stakeholders, with U.S. Environmental Protection Agency-approved laboratory methods used 

whenever possible. Consistent field protocols (with 

documentation) are also suggested. Current methods 

used by the Suffolk County Department of Health 

Services, Nassau County Department of Health, and 

Town of Hempstead are listed in table 4 (in back of 

report).

B. Metadata (information about the data) are important 

for utilization of data and should be documented 

properly. It is recommended that principal investigators of all monitoring programs and studies done in 

the Reserve provide metadata to the NYSDOS or 

the New York State Department of Environmental 

Conservation for archiving in a South Shore Estuary 

Reserve Water Resources database and mapper. By 

supplying metadata, which would include a link to a 

publicly accessible database, results would be more 

easily shared. Potential gaps in monitoring would 

be identified so that proposals could be tailored and 

additional partners involved. Historical data may 

be available in an older standard, and conversion to 

the latest units would be ideal (such as converting 

the elevation datum for water-level measurements 

from the National Geodetic Vertical Datum of 1929 

[NGVD 29] to the North American Vertical Datum 

of 1988 [NAVD 88]). Any conversion performed on 

data should be noted, along with the conversion tool 

used, in the metadata. (Data that are not subject to 

public release because of proprietary or legal obligations would only include principal stakeholder contact information, which would serve as the source of 

data in the metadata provided.)

C. Storage of data collected for a monitoring program 

or study in a manner allowing for researchers and 

stakeholders to access and use findings from previous programs is critical to the efficiency and continuity of studying the Reserve. Long-term datasets 

are valuable for historical context and should be 

preserved after a project ends. Databases maintained 

by the Federal government for the dissemination 

and preservation of environmental data are available at no charge. Two in particular, EPA Storage 

and Retrieval (through the Water Quality Portal) 

and U.S. Geological Survey ScienceBase, provide 

efficient mechanisms by which data, metadata, and 

relevant ancillary information can be shared with 

the public and archived in perpetuity. In addition 

to data storage, a new tool being developed by the 

USGS will be made available to other agencies and 

municipalities for the digitization of paper records 

containing data in a standard template (for example, 

old hand-written field forms) in the near future 

(Wippich, 2012). This online tool will allow records 

to be scanned and electronically formatted to allow 

users to enter the values in text fields representing 

the fields on the paper form—these values are then 

stored in a database and provided to the user.

D. Water-level data recorded in reference to NGVD 29 

should be converted to NAVD 88 and standardized 

in the future. NOAA provides a datum converter, 

available at https://www.ngs.noaa.gov/cgi-bin/

VERTCON/vert_con.prl.

2. Additional real-time water-quality monitoring is needed 

in the bays and tributaries of the Reserve. Real-time 

monitoring stations are costly, and those established as 

part of research projects can often be maintained with 

operations and maintenance funding that is a small 

fraction of the cost to establish the station. In situations where ongoing data collection would be valuable 

for management efforts, a streamlined path to providing continued funding for these stations should be in 

place. Current and recently approved locations and their 

respective constituents can be found on the Coordinated 

Water Resources Monitoring Strategy mapper.

A. The following locations are recommended for realtime tide (stage) and water-quality monitoring and 

could be developed by the Stony Brook University 

School of Marine and Atmospheric Sciences and (or) 

the USGS; these could also serve as early-warning 

stations in the event of a coastal storm: Forge River, 

Robert Moses Bridge, Heady Creek, Tiana Bay, 

Reynolds Channel (buoys to determine flow and 

basic constituents), and additional locations in the 

Great South Bay. (The USGS is currently [2017] 

working with State and Federal partners to install 

tide gages in Shinnecock Bay and Moriches Bay.)

B. Additional constituents, such as nutrient loading 

(nitrate) and water clarity (turbidity and [or] photosynthetically active radiation), to the current surface 
44 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

water-quality network are recommended for existing sites because they would support management 

decisions and fulfill recommendations made in other 

management and action plans already in place. Support for these constituents could come from TNC 

and (or) the NYSDEC to supplement data collection 

in areas of seagrass restoration efforts.

3. Coordinate research and agency monitoring programs 

with citizen science organizations to establish a Reserve 

report card and support total maximum daily load development.

A. Researchers from the National Oceanic Atmospheric 

Administration and the University of Maryland 

Center for Environmental Science have developed 

a reporting system that uses six core trophic state 

indicators to grade the conditions of an estuary with 

respect to ecological health (Bricker and others, 

2007; EcoCheck, 2011). If the reporting system were 

adopted for use in the Reserve, conditions would be 

graded on the basis of physical (water clarity and 

submerged aquatic vegetation survey) and chemical 

(dissolved oxygen, water temperature, nitrogen and 

phosphorus, and chlorophyll a) data and the availability of data. The waters should be divided into 

segments such that each can be monitored at specific 

locations where changes in practice or infrastructure 

can be made. Additional constituents monitored are 

those identified by management plans and those 

affected by a potential change (for example, stormwater runoff being diverted to bioswales would be 

evaluated for major ions and trace metals, nutrients, 

and fecal indicator bacteria). Sampling regimes 

should be created on the basis of factors outlined in 

EcoCheck (2011), and the shared sampling effort 

should be coordinated by the Reserve Office. This 

reporting system would be a simplified graphical 

product to raise community awareness and help 

describe the issues identified by management plans 

in an easy-to-understand way.

B. Many tributaries within the Reserve are listed on the 

303(d) list of impaired waters and TMDLs. Citizen 

scientists could conduct supplemental nutrient and 

pathogen monitoring to support the creation of a 

TMDL. It is important to synchronize current monitoring programs and establish new stations in areas 

where nitrogen and pathogen sources are known 

but not assessed (for example, storm drain outfalls). 

Following an established quality assurance project 

plan (QAPP) for the collection of water samples, 

volunteers would submit samples through an agreement with either a private lab (similar to the monitoring program established by the Friends of the Bay 

(Oyster Bay) or a local academic institute. Further, 

handheld equipment, such as spectrofluorometers, 

could be used onsite to determine various forms of 

nitrogen and phosphorus—several analytical test kits 

for spectrofluorometers are available that have been 

approved by the EPA—and coliform concentrations 

(for example, the Colifast field meter).

4. Municipal-land-use maps should be updated every five 

years because changes in development density, development type, and land preservation directly affect the 

ecological health of the Reserve. Resources at the town 

and county levels have been strained, which has led to 

fewer revisions to land-use and other maps and products. 

Coordinating the development and storage of a GIS and 

remote sensing repository (New York State GIS clearinghouse, for example [http://opdgig.dos.ny.gov/#/home]) 

for Reserve-related data could be achieved by working 

with university professors and nonprofit organizations. 

Professors from Hofstra University, Molloy College, and 

Adelphi University have indicated their organizations 

have the capacity to work together and with the towns 

and counties to update and improve land-use maps (or 

coverages) and incorporate other infrastructure products 

(for example, locations of onsite wastewater treatment 

systems) that are necessary for proper planning around 

sensitive and impaired waters and in contributing areas. 

These updated maps are of particular importance in areas 

that expect major redevelopment that would change the 

current wastewater footprint of an area. Cataloging the 

locations of stormwater BMPs that include green infrastructure in the watersheds within the Reserve is another 

area for towns and counties to collaborate with universities, as each municipality typically has its own records 

and ways in which the projects are monitored for permit 

compliance and efficiency.

5. Remote sensing technology, such as lidar topobathy, aerial fluorescence, and unmanned aircraft and submersibles 

(drones), continues to advance in accuracy and precision 

and can provide large-scale coverage that is needed for 

assessing system-wide processes and thus should be 

used to collect data in conjunction with relevant projects 

as often as permitted to allow for continuous updates 

to the dataset. These data should be cataloged by the 

Reserve Office, made available through the New York 

State GIS Clearinghouse, and referenced by the data.

gov website so they are available to other researchers 

and organizations. Although costs can be high, the data 

these tools provide allow for estuary-wide surveys of 

shoreline movement, vegetation, and bathymetry that 

inform models and planning efforts. It is recommended 

that the shoreline monitoring of sediment transport 

and mapping of topography be continued through local 

agreements with organizations that monitor the Reserve 

and the FWS and NOAA. Unprotected shorelines 

(including along streams), wetlands, and marsh island 

extents should be monitored jointly by towns, counties, 

and nonprofit organizations for changes, such as marsh 
General and Coordination Recommendations From the Project Advisory Committee 45

loss or accretion, and effects of sea-level rise. Further, 

monitoring of aquatic vegetation (such as eelgrass and 

Ruppia maritima [widgeongrass]) through aerial imagery (collected by the FWS) should be coordinated with 

seabed surveys and SET data collections to calibrate the 

remote sensing equipment, inform subsequent models, and maintain a consistent dataset. (SAV data are a 

trophic state indicator and required to create the Reserve 

report card.) The effort can be coordinated through the 

Reserve Office, which could provide opportunities for 

researchers and other stakeholders to request an opportunity to collaborate during a data collection period. Field 

verification of remote data should also be coordinated. 

Specific recommendations include the following:

A. Satellite-acquired bathymetric data do not provide 

the resolution needed to track the low sedimentation 

rates of the Reserve bays. Therefore, autonomous 

underwater vehicles or boat-mounted sensors are 

recommended for detailed surveys and should be 

deployed in segments throughout the Reserve.

B. Aerial imagery should be acquired every 3–5 years 

and after a major coastal storm that causes considerable sediment redistribution or infrastructure 

damage.

C. Invasive species surveys conducted by municipalities, citizen scientists, and other organizations should 

be correlated with remote imagery.

6. Advanced hydrodynamic models are available to help 

inform management decisions related to contaminant 

loading to the bays and groundwater under a variety of 

conditions and could be employed to improve understanding of contaminant loading to the Reserve. Models 

applicable to the Reserve watershed include the updated 

USGS groundwater traveltime model, stormwater loading models such as SPARROW (https://water.usgs.gov/

nawqa/sparrow/), EPA Virtual Beach (https://www.epa.

gov/exposure-assessment-models/virtual-beach-vb), and 

numerical models for circulation and water movement 

throughout the estuary. Data should be collected for 

input conditions to support model development, such as 

NOAA bathymetry, shoreline dimensions, tributary flow 

data, and a sufficient water-quality dataset. As the models being proposed for groundwater flow and nutrient 

loading are island wide, the NYSDEC and the NYSDOS 

intend to evaluate the current groundwater and surfacewater sampling programs to be sure the necessary data 

are being collected at the resolution, frequency, and 

accuracy to account for contributions, particularly when 

changes are implemented.

7. New York State should adopt a decision support tool for 

use with groundwater and nutrient loading data collected 

and modeled in Long Island. One option is Watershed 

MVP (http://www.watershedmvp.org), created by the 

Cape Cod Commission, which has been offered to New 

York State. This product would be a valuable interface 

for visualizing changes to land practices concerning 

nutrient loading (wastewater infrastructure improvements, changes in fertilizer application, and stormwater 

runoff diversion). A USGS model for delineating refined 

areas contributing to groundwater recharge (currently 

under development) would be used as the backbone of 

the hydrodynamics of groundwater flow to the tributaries 

and bays. Also needed are nutrient loading and assessment models scheduled to be developed under the Long 

Island Nitrogen Action Plan (LINAP). In order to support these nutrient models, surface-water- and groundwater-quality monitoring data are needed. As is being 

proposed through the LINAP, constituents necessary to 

inform the models used by the tool should be determined 

by forming a committee and assessing what needs to be 

collected and by which organizations.

8. A network of rapid-deployment water-quality monitors 

for responding ahead of a major coastal storm would 

provide emergency responders with data needed to protect public health and would enable testing of recently 

developed particle-transport models (Swanson, 2013) 

and developing new models. This network could leverage the USGS Surge, Wave, and Tide Hydrodynamics 

(SWaTH) network (https://water.usgs.gov/floods/swath/) 

locations. Collaboration on the Federal, State, and local 

levels could help supplement the lack of permanent, continuous water-quality monitoring to assess the release of 

sewage, runoff, and other contaminants to the bays and 

tributaries. Little is known of the short- and long-term 

effects these releases had on the Reserve ecosystem in 

the aftermath of Hurricane Sandy.

9. As Suffolk County legislation moves to approve 

wastewater-treatment upgrades (both onsite and community), coordinating the groundwater-quality sampling 

is recommended in order to develop trends in the upper 

glacial and Magothy aquifers, as well as the bays and 

tributaries of the Reserve. Advanced onsite wastewater 

systems installed in priority areas within the Reserve 

boundaries (Suffolk County Government, 2015), particularly over a large area, could result in major changes 

to the concentration of nutrients loading to the Reserve 

(Monti and Scorca, 2003). Developing a baseline at this 

early stage is critical to understanding what works in 

Long Island soils and hydrology when before-and-after 

installation comparisons are made. Data collected by 

advanced onsite wastewater-treatment-system vendors 

and service providers should be centralized in a database and made available publicly for calibrating inputs 

to models and comparing removal efficiencies among 

systems and across the region. Current monitoring that 

provides a baseline includes the USGS groundwater- and 

surface-water-quality network, SCDHS Office of Water 

Resources, SCDHS Office of Ecology sampling, Nassau 
46 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

County Department of Health sampling, and Town of 

Hempstead sampling.

10. The Community Preservation Fund should be instated 

throughout Long Island as it has been successful in 

preserving open spaces within the Peconic Estuary and 

has recently (2016) been approved by voters to use some 

of its funds to assess water quality. A similar transfer tax 

for public purchases of south shore properties has been 

attempted in the western towns of the Reserve (Babylon, 

Islip, and Brookhaven), but the legislation must still 

pass a referendum. Retaining lands and keeping nature 

preserves open provides protected habitat, and restoration of wetlands provides buffering for storm surge and 

increased resiliency over hardened structures such as 

bulkheads. Preserved lands would also be suitable for 

research and water-quality and ecological monitoring 

with respect to understanding implications of conservation and reclamation of developed land and protection of 

groundwater and surface waters.

11. Effects of diverting the Bay Park and Long Beach 

sewage treatment plants discharge to the Cedar Creek 

Water Pollution Control Plant line (and thereby increasing discharge from the current ocean outfall) need to 

be investigated. Rigorous baseline data (for example, 

pH, water temperature, nitrogen [inorganic species as 

well as total inorganic and total organic] concentration, 

and Ulva surveys [within the bays]) should be collected 

within Reynolds Channel and the bays, as well as at 

the proposed current ocean outfall for Cedar Creek, 

before modifications are made and maintained after 

construction to track potential effects on water quality 

in the Reserve through time. This sampling effort would 

require commitments from the Town of Hempstead, Nassau County, the NYSDEC, and the EPA, and coordination with the Reserve Office and other researchers would 

be important.

12. A unified system to document long-term water-quality 

improvements resulting from wastewater-infrastructure 

upgrades, BMP and stormwater mitigation, and coastal 

reconstruction and resiliency projects is needed for 

the Reserve. In particular, a website with interactive 

mapper to display current infrastructure projects (with 

metadata to include agencies involved, type of grant, 

and waterways affected) and the respective monitoring 

locations and types is needed. A commitment to periodic 

monitoring should be part of future grant requirements 

for infrastructure and coastal improvements, and a 

centralized repository at the State or Federal level should 

hold results.

Recommendations for Stakeholder Coordination 

by the Project Advisory Committee

Consistent documentation of resource monitoring and 

other scientific activities within the Reserve by the Reserve 

Office would improve coordination and efficiency and address 

management issues presented in previous plans and strategies. The Reserve Office should consider reestablishing its 

role as the main point of coordination for groups conducting 

volunteer monitoring as a way of assisting agencies or other 

organizations to enhance current monitoring programs. The 

Reserve Office could provide information and standardized 

QAPPs, coordinate monitoring among groups to maximize 

efficiency, and help with the EPA citizen science equipment 

loaner program. This monitoring is needed in areas the towns 

and counties are unable to sample on a consistent basis and 

can help fulfill recommendations made in the 2000 CWRMS 

(that samples be collected at each tributary mouth and along 

each bay and inlet). A full-time coordinator would allow for 

projects to be better synchronized with current management 

needs and with each other and would assume the following 

responsibilities:

• Establish regular meetings of the Reserve Council 

and subcommittees to address all the issues, concerns, 

research gaps that were identified in this CWRMS and 

other management plans. Working group subcommittees should be established to focus on specific issues, 

for example sediment and a horseshoe crab permit 

system.

• Maintain a dynamic list of stakeholders and researchers in concert with the Reserve Council and request 

routine updates (annually through online surveys) that 

capture the current status of monitoring, data interpretation and archival, coordination efforts with other 

stakeholders, and future plans—a forum for stakeholders could be used. 

• Develop a timeline for revision to the CWRMS.

• Determine costs needed to establish a monitoring committee. The Nassau County Soil and Water Conservation District could conduct outreach for municipalities 

with municipal separate storm sewer systems (MS4) 

through committee funding (north shore committees 

have worked well to meet MS4 regulations when budgets are limited). Peconic Estuary now has a Protection 

Committee with members representing towns, Suffolk 

County, and villages.

• Assist citizen scientists, school groups, and other nonprofit organizations collecting useful data by providing 

resources for sample collection and monitoring, as well 

as assisting the creation of quality assurance and quality control (QA/QC) protocols consistent with the level 

of scrutiny the data will receive.
Coordinated Water Resources Monitoring Strategy Website 47

• Look for ways to leverage monitoring already being 

conducted (or that is planned) by municipalities, academia, volunteers, and the Soil and Water Conservation Districts and apply them to existing management 

plans while working with the communities to garner 

support and assess opportunities for citizen science to 

fill gaps.

• Conduct public outreach by presenting a summary of 

the data collected within the Reserve and how they 

coalesce into usable information.

• Hold workshops for citizen science groups on topics 

such as water-quality monitoring equipment, and provide technical advice on the way in which a monitoring program should be set up. The workshops should 

emphasize standardizing data collection and maintaining proper field and calibration notes.

• Assist and encourage those collecting data to input 

their data into dedicated citizen science databases or 

a Federal repository (such as Water Quality Portal or 

USGS ScienceBase) as a way of archiving the record 

and ensuring the data are available to the public via the 

internet and the CWRMS mapper.

• Distribute resources, such as templates for necessary 

documents (for example, QAPPs), report and data 

entry forms, and applications for equipment loaner 

programs.

• Encourage and assist in opening up dialogue concerning issues, monitoring, and opportunities among 

Reserve stakeholders. This could be done through a 

consortium of academics that would review current 

data on a regular basis and generate reports on the 

health of the Reserve in concert with the report cards. 

More presentations and a venue for discussion of 

Reserve issues, monitoring, and opportunities would 

help raise awareness in the communities and with 

politicians. The consortium needs to be independent 

of policymakers and yet integrative into oversight by 

regulatory agencies.

• Maintain an up-to-date list of opportunities (State and 

Federal) for grants related to the management topic at 

hand and work to coordinate monitoring among scientists, researchers and students, as well as bringing in 

government agencies (Federal, State, Tribal, town and 

village) to help bolster the data collection effort and 

support effective grant proposals.

Coordinated Water Resources 

Monitoring Strategy Website

The Coordinated Water Resources Strategy website 

(http://www.sserwaterquality.us/) was created to provide 

information about current and upcoming water-quality and 

ecological monitoring in the Reserve. Its main purpose is to 

host an interactive mapper through the duration of the project 

by which stakeholders and interested parties can assess the 

extent of monitoring programs and identify potential gaps in 

the current programs from a geographical perspective. A brief 

description of the coordination effort and the final version 

of this report are available from the main “CWRMS” web 

page. Monitoring programs are displayed with additional 

information on the “Data” web page and through toggling 

and querying on the mapper. The “References” web page lists 

relevant documents, such as management reports, action plans, 

and research papers, in a searchable format. A list of Reserve 

stakeholders that participated in the development of the 

2016–17 CWRMS as part of the Project Advisory Committee 

is provided on the “Stakeholder” web page. A forum that was 

established for PAC members to share information and post 

documents and data for dissemination on the main CWRMS 

website is reached by clicking on “Login”—this function 

is limited in use to PAC members and will not be preserved 

beyond the end of this project unless the scope is expanded to 

include additional estuaries in Long Island (see the report sections “General and Coordination Recommendations From the 

Project Advisory Committee” and “Potential Expansion”).

Currently (2017), the CWRMS website resides on a thirdparty server and is operated and maintained by the USGS. The 

USGS ScienceBase entry (https://doi.org/10.5066/F7JQ0Z46) 

for this project will ultimately host the resources currently 

available on the CWRMS website, as well as links to download this report and associated tables, the interactive mapper, 

and the information associated with the mapper and report. 

Functions of the website and the databases that serve the mapper will be preserved, as the coding has been developed by the 

USGS and is open source. The entire website conforms to the 

Rehabilitation Act of 1973 and is 508 compliant (U.S. Access 

Board, 2000). Current and past news related to water-quality 

issues in the Reserve available on the “SSER” web page are 

available through the Reserve Council website (http://www.

dos.ny.gov/opd/sser/).

Resources and Data

Documents related to water and biological studies done 

within the Reserve over the past 16 years have been compiled to supplement the resources referenced in the 2000 

CWRMS report. Those references, along with the more recent 
48 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

comprehensive management plans of watersheds and bays, 

updated study and model information, and climate change and 

resiliency plans, are referenced in the CWRMS report and are 

available for download. Links to websites are also provided, 

and the database can be sorted and queried to help users find 

resources by topic, waterbody, or funding agency.

The “Data” web page provides information available on 

the interactive mapper in a tabular format that can be sorted 

and searched. Metadata provided by organizations conducting 

water-quality and ecological monitoring programs, wildlife 

studies, and infrastructure are important for understanding 

ecosystem health and where water-quality monitoring occurs 

(such as outfall locations of storm drains and New York State 

Department of Environmental Conservation shellfish classification areas). Information on data ownership and contact 

information is available. Tables displayed that result from sorting and queries can be downloaded. If datasets were uploaded 

by an organization for dissemination (because the data would 

not otherwise be available publicly, for example), those data 

are available for download directly (with the disclaimer that 

data were not collected or evaluated by the NYSDOS or 

USGS and these agencies take no responsibility for their quality or use).

Mapper

The Reserve mapper aggregates available monitoring, 

study, and resiliency information from government agencies, 

academic institutions, nonprofit organizations, and citizen scientists and displays basic information about the type of monitoring, constituents collected, and responsible party contact or 

link by which data can be requested or downloaded (fig. 5). 

The mapper and metadata tables are meant to be dynamic and 

continuously updated on the basis of changes in monitoring 

programs (for example, addition of constituents measured) 

and implementation of new studies or monitoring. In order for 

these continuous updates to be successful, the Reserve Office 

should be provided with updated versions of the spreadsheets 

used in the initial information-gathering for this report. The 

annual update request sent to the Reserve Office could be 

enhanced by use of this spreadsheet through the use of an 

online form (as suggested in the section “Quality Assurance 

and Quality Control, Metadata, and Data Archives”).

Metadata Attributes

As presented in the section “Quality Assurance and 

Quality Control, Metadata, and Data Archives,” monitoring 

resources can be divided by class, type, and frequency of sampling. The mapper defaults to displaying the data categorized 

by sample environment (class); that is, water (surface water, 

groundwater, and sediment) and biological (wildlife surveys, 

HABs, pathogens), with subsets for each being represented 

by different point shapes and colors. Subcategories represent 

details of a program, such as frequency of sample collection 

(real-time or discrete measurements, for example) and constituent class (such as water-quality samples collected for 

physical constituents and pesticide analysis). Presentation of 

the metadata through information boxes has been standardized 

across classes to include only attributes relevant to understanding the name of the study or program, the type of data 

available, the quality of the data (QA/QC; if applicable), and 

the location of each site (coordinates with respective datum). 

Standardizing these fields allows for information within each 

class and type to be filtered and thus enables the mapper to 

function properly.

Functionality

The mapper uses the Esri ArcGIS platform, which has 

been customized by using Java script to allow for integration and searchability of the metadata provided. Points that 

represent monitoring programs (water-quality or ecological) 

or studies are generated from an array of tables extracted 

from the South Shore Estuary Reserve CWRMS monitoring 

network database. Displaying points specific to a search or 

query is done by filtering select criteria within a given subset 

of the metadata. Information provided by PAC members 

was categorized on the basis of several attributes: resource 

type (environmental data, infrastructure details, geographic 

coverages, or resiliency plans), status of program (historical record or ongoing), and responsible organization (data 

or project owner). Attribute tables that display when a point 

or layer is selected on the mapper have been standardized 

on the basis of the resource type to provide the same type of 

information needed to compare monitoring programs, types 

of infrastructure and associated environmental impact data 

(for example, State Pollutant Discharge Elimination System 

permits), ecological assessments or studies, source of information (that is, the owner), and contact for obtaining data or GIS 

layers. The Reserve CWRMS monitoring network database is 

served through the website host, with copies backed up on the 

USGS server.

Polygons are presented through a service from the USGS 

ScienceBase, are generated from existing layers, and are incorporated into the search and navigation functions. These layers 

can be toggled on and off and include links to associated 

information on the USGS server. Search functions are possible but limited in the service-generated layers. Navigation of 

the mapper includes functions similar to many of the popular 

online mappers (zoom, pan, change base layer) and allows for 

search by hydrological unit code (base 12; HUC12), address, 

and waterbody.

Potential Expansion

The process by which program and study information 

within the Reserve was gathered from stakeholders can be 

replicated for the other two estuaries around Long Island—

Peconic Estuary and Long Island Sound. One component of 
Coordinated Water Resources Monitoring Strategy Website 49 Figure 5. The South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy website mapper. 
50 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

the NYSDEC LINAP is to assemble all available data for use 

in future models that rely on new and historical data for nutrient concentrations assessed in surface waters, in groundwater, 

and from loading models. Simple, standardized templates are 

directly incorporated into the mapper and data features on 

the website, and the USGS has the capacity to incorporate 

additional programs, watersheds, and data layers on the basis 

of LINAP and stakeholder needs.

References Cited

A Day in the Life, [n.d.], List of participating rivers and sites: 

A Day in the Life website, accessed April 10, 2017, at 

http://www.portaltodiscovery.org/aday/sites.htm.

AKRF Inc., 2015, Framework for the future—Suffolk County 

comprehensive master plan 2035: Hauppauge, N.Y., Suffolk 

County Department of Economic Development and Planning, 692 p.

Aretxabaleta, A.L., Butman, Bradford, and Ganju, N.K., 2014, 

Water level response in back-barrier bays unchanged following Hurricane Sandy: Geophysical Research Letters, 

v. 41, no. 9, p 3163–3171.

Arthur, Jody, 2015, General guidance for the Office of Water 

Quality external data framework: Indiana Department of 

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Tables 4A–B

Table 4. List of water-quality and ecological monitoring programs ongoing or completed since 2000 

in the South Shore Estuary Reserve, New York, with information on A, objectives and constituents 

and B, quality assurance and quality control, timeframes, and URLs.
60 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 4A. List of water-quality and ecological monitoring programs ongoing or completed since 2000 in the South Shore Estuary Reserve, with information on objectives and constituents. [Names and details related to the monitoring programs provided by the responsible organization. Constituents collected are abbreviated per table 1, with details also provided. DO, dissolved oxygen; TMDL, total maximum daily load; NYSDEC, New York State Department of Environmental Conservation; SoMAS, School of Marine and Atmospheric Sciences; Reserve, South Shore Estuary Reserve; TNC, The Nature Conservancy; SAV, submerged aquatic vegetation; VOC, volatile organic compound; PCB, polychlorinated biphenyl; PAH, polycyclic aromatic hydrocarbon; RSCO, recommended soil cleanup objec- tives; TBT, tributyltin; PSP, paralytic shellfish poisoning; --, not available or not applicable] Monitoring program Organization Level Objectives Constituents collected Constituent details Water/weather monitoring New York State Marine Education Association Academic Collection of weather and water- quality data throughout the Reserve AT, PRECIP, WEATHER, WT, SAL, DO, NO3, NH4, TP, pH Air temperature, humidity, precipitation, cloud cover, cloud type, wind-speed, wind direction, water temp, water density, salin- ity, dissolved oxygen, nitrate, ammonia, phosphate, pH Study of DO & Nutrients on the Patchogue & Carmans River Dowling College Academic Determining long-term water- quality conditions in Long Island estuaries DO, pH, SAL, NUT, WT Dissolved oxygen, pH, salinity, nitrogen and phosphorus, and temperature The Center for Environ- mental Research and Coastal Oceans Moni- toring Molloy College Academic Determining long-term water- quality conditions in Long Island estuaries DO, pH, SAL, CLAR, WT, FIB Dissolved oxygen, pH, salinity, clarity, total and fecal coliforms, and temperature Flow dynamics and water quality Stony Brook Univer- sity SoMAS (Larry Swanson) Academic Model hydrodynamics in the Reserve bays for understanding contaminant transport WVE, RADIO Current, radioisotopes News12 water quality index Stony Brook Univer- sity SoMAS (Chris Gobler) Academic Inform about the quality of the water around Long Island WT, DO, CLAR, FIB, CHL, NA/HAB Temperature, dissolved oxygen, clarity, fe- cal coliform, chlorophyll, harmful algal blooms Great South Bay Project Stony Brook Univer- sity SoMAS (Charlie Flagg) Academic Gain a thorough understanding of the biogeochemistry of the Bay and its effect on pelagic and benthic communities WT, SAL, WL, CHL, TURB, PHOTO Temperature, salinity, sea level, chlorophyll, turbidity, aerial photographs of breach LI Shore Stony Brook University SoMAS (Tom Wilson) Academic Real-time observatory system collecting and distributing sea, bay, and shoreline conditions for Long Island PRECIP, AT, WEATHER, WT, WL, SAL, CHL, TURB, PAR, DO, PHO- TO. FLOW, WVE, WVH 

in past, data in public archive

Hydrographic and meteorological data; 

panoramic image sets, panoramas, and time lapse videos of shorefronts and inlets

Estuarine ecological study Cornell Cooperative 

Extension Marine Program

Academic Development of eelgrass and 

bay scallop restoration plan in Shinnecock Bay, Flanders Bay, Shelter Island Sound, Sag Harbor Bay, and Hewlett Bay

SAV, MA, PS, WT, SHELLS Seeding recruitment, presence of SAV/

macroalgae, sediment grain size, water temperature, scallop presence/absense, and scallop size

Sediment-quality monitoring Stony Brook Univer- sity SoMAS (Bruce 

Brownawell)

Academic Characterize sediment quality in 

Hempstead Bay with regard to wastewater impacts

CEC, PPOL, TOC, TON, 

PART, BS, MP

Quaternary ammonium compounds, metals, 

total organic carbon, total organic nitrogen, grain size, microplastics in bed sediment
Table 4 61

Table 4A. List of water-quality and ecological monitoring programs ongoing or completed since 2000 in the South Shore Estuary Reserve, with information on objectives and constituents.—Continued[Names and details related to the monitoring programs provided by the responsible organization. Constituents collected are abbreviated per table 1, with details also provided. DO, dissolved oxygen; TMDL, total maximum daily load; NYSDEC, New York State Department of Environmental Conservation; SoMAS, School of Marine and Atmospheric Sciences; Reserve, South Shore Estuary Reserve; TNC, The Nature Conservancy; SAV, submerged aquatic vegetation; VOC, volatile organic compound; PCB, polychlorinated biphenyl; PAH, polycyclic aromatic hydrocarbon; RSCO, recommended soil cleanup objectives; TBT, tributyltin; PSP, paralytic shellfish poisoning; --, not available or not applicable]

Monitoring program Organization Level Objectives Constituents collected Constituent details

Coalition of Educational 

Organizations

South Shore Estuary 

Watch (SSEW)

Citizen Monitor water quality in the 

Reserve surface waters

pH, ALK, SS, CHL, NUT, 

ATOX, FIB, WVE, TURB

pH, alkalinity, suspended solids, chlorophyll a, nutrients, toxics, indicator bacteria, 

current velocity, turbidity

Stormwater/streamgaging 

monitoring

Nassau County Department of Public Works County Monitor streamflow, stage, and water quality throughout Nassau FLOW, DO, pH, SAL, NUT, WT Dry-weather flow and water quality

Drinking water monitoring Nassau County County Assess water supply and susceptibility to contamination WT, PRECIP, WL, PPOL, CEC, ClO4, NO3, FIB Temperature, precipitation, water levels, VOCs, pesticides, pharmaceuticals, perchlorate, nitrate, microbials

Groundwater monitoring Nassau County Department of Public Works County Analyze trends concerning the conditions of groundwater 

resources

ClO4, CEC, PPOL Perchlorates, pharmaceuticals, chloride, 

herbicides

Bathing Beach Water Quality Program Nassau County Depart- ment of Health 

Services

County Inspections and regulation of water quality at bathing beaches NUT, DO, SS, PPOL Nitrogen, phosphorus, dissolved oxygen, silt, sediment, PCBs

Beach monitoring Suffolk County Department of Health 

Services

County Protect public health by maintaining safe beaches and shellfishing FIB E. coli, enterococci

Groundwater monitoring Suffolk County Department of Health 

Services

County Monitoring nitrogen contamination in groundwater WL, CEC, NO3, PPOL, NUT Pharmaceuticals, nitrate, pesticides, VOCs, PAHs, metals, chromium above RSCO, 

asbestos, PAH above RSCO, lead, barium, nutrients

Surface water-quality 

monitoring

Suffolk County Department of Health 

Services

County Water-quality assessment of Beaverdam Creek, Yaphank Creek, 

Little Neck Creek, Carmans River, Connetquot River, Forge River, Grand Canal, Patchogue River, Poospatuck Creek, Willets Creek, and Carlls River

NH3, NO3, TKN, NUT, TP, 

OP, SS, FIB, PPOL, WT, DO, SAL, pH, RADIO, NA/HAB, DEPTH, TURB, SS, CHL

Ammonia, nitrite, nitrate, total nitrogen, total 

dissolved nitrogen, total phosphate, total dissolved phosphate, orthophosphate, total suspended sediments, total fecal and coliform bacteria, VOCs, carbamate pesticides, 

chlorinated pesticides, herbicide metabolites, dactal metabolites, metals, radiologicals, water temperature, dissolved oxygen, 

conductivity, pH

Drinking water quality 

monitoring

Suffolk County Water 

Authority

County Ensure drinking water provided 

satisfy national standards

NO3, PPOL, FIB, CEC Nitrate, pesticides, microbials, VOCs, metals 

(chromium), pharmaceuticals
62 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 4A. List of water-quality and ecological monitoring programs ongoing or completed since 2000 in the South Shore Estuary Reserve, with information on objectives and constituents.—Continued [Names and details related to the monitoring programs provided by the responsible organization. Constituents collected are abbreviated per table 1, with details also provided. DO, dissolved oxygen; TMDL, total maximum daily load; NYSDEC, New York State Department of Environmental Conservation; SoMAS, School of Marine and Atmospheric Sciences; Reserve, South Shore Estuary Reserve; TNC, The Nature Conservancy; SAV, submerged aquatic vegetation; VOC, volatile organic compound; PCB, polychlorinated biphenyl; PAH, polycyclic aromatic hydrocarbon; RSCO, recommended soil cleanup objec- tives; TBT, tributyltin; PSP, paralytic shellfish poisoning; --, not available or not applicable] Monitoring program Organization Level Objectives Constituents collected Constituent details Status and Trends Pro- grams Mussel Watch National Oceanic and Atmospheric Admin- istration (Center for Coastal Monitoring and Assessment) Federal Determination of the Status and Trends of the Blue Mussel and pollution assessment that affect Mussel populations SHELLT, PPOL PAHs, PCBs, DDTs, TBTs, chlorinated pesti- cides, and toxic trace elements in sediment and mussel tissue Water quality and Ecology of Great South Bay National Park Service Federal FIB, DO Fecal coliform concentrations, DO Estuarine water-quality and nutrient-enrichment monitoring National Park Service Federal Monitoring of water-quality data in Great South Bay PAR, TURB, WT, SAL, CHL, DO Attenuation of downwelling photosyntheti- cally available radiation (water clarity), turbidity, water temperature, salinity, chlorophyll a in surface water, dissolved oxygen in bottom water Helicopter monitoring U.S. Environmental Protection Agency Federal Floatable debris survellience for coordinated Beach cleanups LITTER Debris floating and in wetlands along the shoreline Groundwater monitoring U.S. Geological Survey Federal Water quality in shallow ground- water wells of south shore [mainland] Long Island and north shore Fire Island CEC, NUT, WT, DO, pH, SAL, TURB Pharmaceuticals, nutrients, wastewater indica- tor compounds, physical constituents Surface water monitoring U.S. Geological Survey Federal Provide periodic records of water quality and quantity of Reserve tributaries and bays WL, WT, SAL, DO, TURB, CHL, pH, NO4 Water-level elevations, temperature, specific conductance, dissolved oxygen, turbidity, chlorophyll, pH, nitrate Environmental Monitoring Assessment Program U.S. Environmental Protection Agency Federal Monitor and assess the status and trends of ecological resources BS, PPOL, DO, FIB, TOPO Sediment chemistry, sediment toxicity, and water quality (dissolved oxygen, fecal contamination, spatial data) sampling for human and ecological services Fire Island Beach Erosion 

Study

U.S. Army Corps of 

Engineers

Federal Assessment of coastal damage 

and risk management projects

SR, TOPO, VEG Shoreline position data, vegetation mapping, 

topographic mapping

South Shore Estuary Reserve TMDL Monitoring U.S. Geological Survey Federal Provide continuously recorded water-quality data to understand the short-term effects of 

stormwater runoff and other pollution sources

WL, WT, SAL, DO, TURB, 

CHL, pH, NO3

Water-level elevations, temperature, specific 

conductance, dissolved oxygen, turbidity, chlorophyll, pH, nitrate

Groundwater monitoring U.S. Geological Survey Federal Water levels of groundwater providing baseflow to tributaries 

of the Reserve

WL, FLOW Stage and flow
Table 4 63

Table 4A. List of water-quality and ecological monitoring programs ongoing or completed since 2000 in the South Shore Estuary Reserve, with information on objectives and constituents.—Continued[Names and details related to the monitoring programs provided by the responsible organization. Constituents collected are abbreviated per table 1, with details also provided. DO, dissolved oxygen; TMDL, total maximum daily load; NYSDEC, New York State Department of Environmental Conservation; SoMAS, School of Marine and Atmospheric Sciences; Reserve, South Shore Estuary Reserve; TNC, The Nature Conservancy; SAV, submerged aquatic vegetation; VOC, volatile organic compound; PCB, polychlorinated biphenyl; PAH, polycyclic aromatic hydrocarbon; RSCO, recommended soil cleanup objectives; TBT, tributyltin; PSP, paralytic shellfish poisoning; --, not available or not applicable]

Monitoring program Organization Level Objectives Constituents collected Constituent details

Litter removal in Nassau 

south shore bays

Operation SPLASH Nonprofit Keep bays free of debris by 

employing litter traps and clean up trips; debris is categorized, counted, and weighed

LITTER, WT, pH, SAL Litter, water temperature, pH, conductivity

Dissolved oxygen monitoring in Great South Bay 

and Hempstead Bay

The Nature Conservancy Nonprofit Investigate stratification of dissolved oxygen in bays DO Dissolved oxygen

Hard Clam Study The Nature Conservancy Nonprofit Monitor hard clam abundance and 

health on TNC bottomlands

SHELLS, WILD, MACRO Hard clam presence and size, sediment type, 

presence of other species of interest (at a minimum identify to the genus level)

Salt marsh elevation monitoring The Nature Conservancy Nonprofit Monitor changes in salt marsh through time SET Salt marsh elevation at nine sites

Bacteriological water 

quality

NYSDEC shellfish 

growing area certification unit

State Monitor sites throughout the 

Reserve for fecal coliform, temperature, and salinity

FIB, WT, SAL Bacteriological water quality, salinity, temperature

Rotating Intensive Basin 

Surveys

NYSDEC State Assessment of water quality, 

long-term trend analysis, establishment of baseline conditions to inform management 

decisions

WT, SAL, DO, pH, CLAR, 

TURB, CHL, MACRO, PPOL, VEG

Water quality including chemcial/biological 

sampling

Horseshoe crab spawning NYSDEC—Crustaceans 

Unit/Cornell Cooperative Extension

State Assessment of horseshoe crab 

health and abundance

HSC May/June horseshoe crab spawning survey/

shorebird survey

Blue crab trawls NYSDEC—Crustaceans 

Unit/SoMAS

State Surveying of blue crab WILD Blue crab count

NY State Shellfish Land 

Certification Program

NYSDEC State Protecting the health of shellfish 

consumers by conducting sanitary surveys of shellfish lands 

in New York State

-- --

Glass eel surveying NYSDEC—Anadromous Fish State Provide periodic populations of juvenile glass eels in Carmans 

River

WILD Juvenile glass eel survey in Carmans River

Bivalve shellfish harvest 

monitoring

NYSDEC Shellfish 

Management

State Aggregating populations of commericially harvested bivalve 

shellfish

WILD Reported harvest from shellfish dealers
64 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 4A. List of water-quality and ecological monitoring programs ongoing or completed since 2000 in the South Shore Estuary Reserve, with information on objectives and constituents.—Continued [Names and details related to the monitoring programs provided by the responsible organization. Constituents collected are abbreviated per table 1, with details also provided. DO, dissolved oxygen; TMDL, total maximum daily load; NYSDEC, New York State Department of Environmental Conservation; SoMAS, School of Marine and Atmospheric Sciences; Reserve, South Shore Estuary Reserve; TNC, The Nature Conservancy; SAV, submerged aquatic vegetation; VOC, volatile organic compound; PCB, polychlorinated biphenyl; PAH, polycyclic aromatic hydrocarbon; RSCO, recommended soil cleanup objec- tives; TBT, tributyltin; PSP, paralytic shellfish poisoning; --, not available or not applicable] Monitoring program Organization Level Objectives Constituents collected Constituent details Mussel tissue analysis NYSDEC shellfish growing area certifica- tion unit State Analysis of Mussel toxins and plankton in Shinnecock Bay, Timber Point, Robert Moses Beach, and Hempstead Bay SHELLT, PLANK Mussels for PSP analysis and plankton tows for microscopic analysis East and west bay sam- pling survey Town of Hempstead Town Establishing baseline of envi- ronmental conditions and increase understanding of marine processes and estuarine ecosystems WT, SAL, DO, pH, CLAR, TURB, PPOL, NUT, FIB Metals, organics, chlorine, nitrate, total coliforms Shellfish analysis for coli- form bacteria Town of Hempstead Town Post-Hurricane Sandy marine study MA, SAV, WILD, FIB, SHELLT Microalgae/macroalgae, bird life/migration, beach fauna and flora, coliform in shellfish Beach and shellfish closures (in cooperation with DEC and Nassau County) Town of Oyster Bay Town Protect public health by maintain- ing safe beaches and shellfish- ing FIB E. coli, enterococci Eelgrass and Bay Scallop Restoration Planning Project Town of Southampton Town Development of eelgrass and bay scallop restoration plan SAV, MA, VEG, BS, MACRO, WETLAND, PART, WILD Seedling recruitment, presence of SAV/mac- roalgae, predator counts, organic matter content, depth range of existing meadows, nutrient levels, light attenuation, poten- tial for seed yield, average shoot density, canopy height, % cover macroalgae, sedi- ment grain size, water temperature, scallop presence/abscence, scallop size Water-quality monitoring Shinnecock Environ- mental Department Tribal Water quality assessment of sites at Heady Creek, Shinnecock Bay (at the Shore), and WestWoods (Peconic) pH, DO, ORP, SAL, WT pH, dissolved oxygen, oxidation/reduction potential, salinity, water temperature, baro- metric pressure
Table 4 65

Table 4B. List of water-quality and ecological monitoring programs ongoing or completed since 2000 in the South Shore Estuary Reserve, with information on quality assurance and quality control, timeframes, and URLs.[Names and details related to the monitoring programs provided by the responsible organization. Associated quality assurance and quality controls are listed, and tiered ranks assigned based on the extent of quality assurance in lab and field protocols followed/documented: tier 1, data of unknown quality; tier 2, data collected following approved protocol but research-based or unapproved methods; tier 3, data collected and analyzed following approved methods and is legally defensible (see the report section “Proposed Ranking of Data” for more details on ranking). QA/QC, quality assurance and quality control; DO, dissolved oxygen; TMDL, total maximum daily load; NYSDEC, New York State Department of Environmental Conservation; SoMAS, School of Marine and Atmospheric Sciences; Reserve, South Shore Estuary Reserve; EPA, U.S. Environmental Protection Agency; SCWA, Suffolk County Water Authority; --, not available or not applicable]

Monitoring program Organization Associated QA/QC QA/QC rank Year started Year ended (or Ongoing as of 2017) Link

Water/weather monitoring New York State Marine 

Education Association

-- 2 2007 2012 http://www.seagrant.sunysb.edu/nysmea/resources-for-educators-sSELF.php

Study of DO & Nutrients on 

the Patchogue & Carmans River

Dowling College Field meters with QA/

QC documented

2 1997 2005 --

The Center for Environmental Research and Coastal 

Oceans Monitoring

Molloy College -- 2 2004 Ongoing as 

of 2017

http://www.molloy.edu/academics/undergraduate-programs/

biology/cercom

Flow dynamics and water 

quality

Stony Brook University 

SoMAS (Larry Swanson)

Published and experimental methods 2 -- -- --

News12 water quality index Stony Brook University 

SoMAS (Chris Gobler)

-- 2 -- Ongoing as 

of 2017

http://www.stonybrook.edu/happenings/facultystaff/goblerlabs-summer-water-quality-index-reported-on-news-12/

Great South Bay Project Stony Brook University 

SoMAS (Charlie Flagg)

-- 2 2004 Ongoing as 

of 2017

http://po.msrc.sunysb.edu/GSB/

LI Shore Stony Brook University 

SoMAS (Tom Wilson)

Published and experimental methods 2 1998 Ongoing as of 2017 http://www.lishore.org

Estuarine ecological study Cornell Cooperative Extension Marine Program Certified County Lab, certified contract lab 3 2005 2008 http://seagrassli.org/restoration/current_projects.html

Sediment-quality monitoring Stony Brook University 

SoMAS (Bruce Brownawell)

Published and experimental methods 2 2011 Ongoing as of 2017 --

Coalition of Educational 

Organizations

South Shore Estuary Watch 

(SSEW)

-- 1 -- -- --

Stormwater/streamgaging 

monitoring

Nassau County Department 

of Public Works

Certified County Lab, 

certified contract lab

3 -- -- --

Drinking water monitoring Nassau County Certified County Lab, 

certified contract lab

3 1973 1991 --

Groundwater monitoring Nassau County Department 

of Public Works

Certified County Lab, 

certified contract lab

3 1987 Ongoing as 

of 2017

--

Bathing Beach Water Quality Program Nassau County Department of Health Services Certified County Lab, certified contract lab 3 -- Ongoing as of 2017 --
66 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 4B. List of water-quality and ecological monitoring programs ongoing or completed since 2000 in the South Shore Estuary Reserve, with information on quality assurance and quality control, timeframes, and URLs.—Continued [Names and details related to the monitoring programs provided by the responsible organization. Associated quality assurance and quality controls are listed, and tiered ranks assigned based on the extent of qual- ity assurance in lab and field protocols followed/documented: tier 1, data of unknown quality; tier 2, data collected following approved protocol but research-based or unapproved methods; tier 3, data collected and analyzed following approved methods and is legally defensible (see the report section “Proposed Ranking of Data” for more details on ranking). QA/QC, quality assurance and quality control; DO, dissolved oxygen; TMDL, total maximum daily load; NYSDEC, New York State Department of Environmental Conservation; SoMAS, School of Marine and Atmospheric Sciences; Reserve, South Shore Estuary Reserve; EPA, U.S. Environmental Protection Agency; SCWA, Suffolk County Water Authority; --, not available or not applicable] Monitoring program Organization Associated QA/QC QA/QC rank Year started Year ended (or Ongoing as of 2017) Link Beach monitoring Suffolk County Department of Health Services -- 3 Circa 1977 Ongoing as of 2017 https://gisportal.suffolkcountyny.gov/gis/home/item.html?id=a d10b6495e6149efbbda5af8f00bc957 Groundwater monitoring Suffolk County Department of Health Services Certified County Lab 3 Circa 1975 Ongoing as of 2017 -- Surface water-quality moni- toring Suffolk County Department of Health Services Certified County Lab, certified contract lab

3 1977 Ongoing as 

of 2017

https://gisportal.suffolkcountyny.gov/gis/home/item.html?id=a

4793d074dae4c95b43ac95864f0d7a0

Drinking water quality 

monitoring

Suffolk County Water 

Authority

Documented field protocols; EPA-certified 

SCWA lab

3 1960 Ongoing as 

of 2017

--

Status and Trends Programs 

Mussel Watch

National Oceanic and 

Atmospheric Administration (Center for Coastal 

Monitoring and Assessment)

Documented field protocols; EPA-certified lab

3 1986 Ongoing as 

of 2017

https://products.coastalscience.noaa.gov/collections/ltmonitoring/nsandt/

Water quality and Ecology 

of Great South Bay

National Park Service -- -- 1989 2002 http://irmafiles.nps.gov/reference/holding/441221?accessType

=DOWNLOAD

Estuarine water-quality 

and nutrient-enrichment monitoring

National Park Service Documented field protocols

3 2006 2011 http://science.nature.nps.gov/im/units/ncbn/monitor/estuaries.

cfm

Helicopter monitoring U.S. Environmental Protection Agency Documented field pro- tocols

3 2013 -- --

Groundwater monitoring U.S. Geological Survey Documented field protocols; EPA-certified lab

3 1938 Ongoing as 

of 2017

http://waterdata.usgs.gov/nwis/gw

Surface water monitoring U.S. Geological Survey Documented field protocols; EPA-certified lab

3 Ongoing as 

of 2017

http://waterdata.usgs.gov/nwis/

Environmental Monitoring 

Assessment Program

U.S. Environmental Protection Agency Documented field proto- cols; EPA-certified lab

3 1990 2006 https://archive.epa.gov/emap/archive-emap/web/html/

Fire Island Beach Erosion 

Study

U.S. Army Corps of Engineers Documented field pro- tocols; EPA-certified 

labs

3 -- -- http://www.nan.usace.army.mil/Missions/Civil-Works/

Projects-in-New-York/Fire-Island-to-Montauk-Point-Reformulation-Study/

South Shore Estuary Reserve 

TMDL Monitoring

U.S. Geological Survey Documented field protocols; EPA-certified lab

3 2004 Ongoing as 

of 2017

https://www.sciencebase.gov/catalog/

item/560155fde4b03bc34f544447
Table 4 67

Table 4B. List of water-quality and ecological monitoring programs ongoing or completed since 2000 in the South Shore Estuary Reserve, with information on quality assurance and quality control, timeframes, and URLs.—Continued[Names and details related to the monitoring programs provided by the responsible organization. Associated quality assurance and quality controls are listed, and tiered ranks assigned based on the extent of quality assurance in lab and field protocols followed/documented: tier 1, data of unknown quality; tier 2, data collected following approved protocol but research-based or unapproved methods; tier 3, data collected and analyzed following approved methods and is legally defensible (see the report section “Proposed Ranking of Data” for more details on ranking). QA/QC, quality assurance and quality control; DO, dissolved oxygen; TMDL, total maximum daily load; NYSDEC, New York State Department of Environmental Conservation; SoMAS, School of Marine and Atmospheric Sciences; Reserve, South Shore Estuary Reserve; EPA, U.S. Environmental Protection Agency; SCWA, Suffolk County Water Authority; --, not available or not applicable]

Monitoring program Organization Associated QA/QC QA/QC rank Year started Year ended (or Ongoing as of 2017) Link

Groundwater monitoring U.S. Geological Survey Documented field protocols; EPA-certified lab 3 1938 Ongoing as of 2017 http://waterdata.usgs.gov/nwis/gw

Litter removal in Nassau 

south shore bays

Operation SPLASH -- 1 1990 Ongoing as 

of 2017

http://www.operationsplash.net/

Dissolved oxygen monitoring in Great South Bay 

and Hempstead Bay

The Nature Conservancy -- 2 -- Ongoing as 

of 2017

http://www.nature.org/ourinitiatives/regions/northamerica/

unitedstates/newyork/index.htm?src=sea.AWP.prnone.crv1&kt=natureconservancy&gclid=CNav3aur5M0CFc8lgQoded0CtA

Hard Clam Study The Nature Conservancy -- 2 2004 Ongoing as 

of 2017

http://www.nature.org/ourinitiatives/regions/northamerica/

unitedstates/newyork/index.htm?src=sea.AWP.prnone.crv1&kt=natureconservancy&gclid=CNav3aur5M0CFc8lgQoded0CtA

Salt marsh elevation monitoring The Nature Conservancy -- 2 2011 Ongoing as of 2017 http://www.nature.org/ourinitiatives/regions/northamerica/ unitedstates/newyork/index.htm?src=sea.AWP.prnone.crv1

&kt=natureconservancy&gclid=CNav3aur5M0CFc8lgQoded0CtA

Bacteriological water quality NYSDEC shellfish growing 

area certification unit

-- 3 1920 Ongoing as 

of 2017

--

Rotating Intensive Basin 

Surveys

NYSDEC -- 3 1999 Ongoing as 

of 2017

http://www.cnyrpdb.org/oneidalake/programs/monitoring/ribs.

asp

Horseshoe crab spawning NYSDEC—Crustaceans 

Unit/Cornell Cooperative Extension

-- 3 2005 Ongoing as 

of 2017

http://www.dec.ny.gov/about/796.html

Blue crab trawls NYSDEC—Crustaceans 

Unit/SoMAS

-- 3 2014 Ongoing as 

of 2017

http://www.dec.ny.gov/about/796.html

NY State Shellfish Land 

Certification Program

NYSDEC -- 3 -- -- http://gcmd.nasa.gov/KeywordSearch/Metadata.do?Portal=GC

MD&KeywordPath=DataCenters%7CU.S.+STATE%2FREGIONAL%2FLOCAL+AGENCIES%7CNEW+YORK&OrigMetadataNode=GCMD&EntryId=gomc_231&MetadataView=Full&MetadataType=0&lbnode=mdlb3
68 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 4B. List of water-quality and ecological monitoring programs ongoing or completed since 2000 in the South Shore Estuary Reserve, with information on quality assurance and quality control, timeframes, and URLs.—Continued [Names and details related to the monitoring programs provided by the responsible organization. Associated quality assurance and quality controls are listed, and tiered ranks assigned based on the extent of qual- ity assurance in lab and field protocols followed/documented: tier 1, data of unknown quality; tier 2, data collected following approved protocol but research-based or unapproved methods; tier 3, data collected and analyzed following approved methods and is legally defensible (see the report section “Proposed Ranking of Data” for more details on ranking). QA/QC, quality assurance and quality control; DO, dissolved oxygen; TMDL, total maximum daily load; NYSDEC, New York State Department of Environmental Conservation; SoMAS, School of Marine and Atmospheric Sciences; Reserve, South Shore Estuary Reserve; EPA, U.S. Environmental Protection Agency; SCWA, Suffolk County Water Authority; --, not available or not applicable] Monitoring program Organization Associated QA/QC QA/QC rank Year started Year ended (or Ongoing as of 2017) Link Glass eel surveying NYSDEC—Anadromous Fish -- 3 2000 Ongoing as of 2017 -- Bivalve shellfish harvest monitoring NYSDEC Shellfish Man- agement -- 3 1946 Ongoing as of 2017 -- Mussel tissue analysis NYSDEC shellfish growing area certification unit -- 3 2000 Ongoing as of 2017 -- East and west bay sampling survey Town of Hempstead -- 3 1975 Ongoing as of 2017 https://www.toh.li/conservation-and-waterways Shellfish analysis for coli- form bacteria Town of Hempstead -- 3 1978 -- https://www.toh.li/conservation-and-waterways Beach and shellfish closures (in cooperation with DEC and Nassau County) Town of Oyster Bay -- 3 -- Ongoing as of 2017 -- Eelgrass and Bay Scallop Restoration Planning Project Town of Southampton -- -- 2005 2008 http://www.seagrassli.org/restoration/current_projects.html Water-quality monitoring Shinnecock Environmental Department -- -- 2014 Ongoing as of 2017 --
Appendixes 1–5

Appendix 1 71

Appendix 1. Updates to Recommendations Presented in the 2000 Coordinated

Water Resources Monitoring Strategy

Mullaney, J.R., and Schwarz, G.E., 2013, Estimated nitrogen 

loads from selected tributaries in Connecticut draining to 

Long Island Sound, 1999–2009: U.S. Geological Survey 

The statuses of recommended improvements presented 

in the appendix tables of the 2000 Long Island South Shore 

Estuary Reserve Coordinated Water Resources Monitoring 

Strategy (CWRMS) to the then-current monitoring programs 

within the South Shore Estuary Reserve have been checked 

and are presented in the following tables. The status of each 

recommendation has been marked as either “Not done,” “Partially done,” “Done,” or “Unknown” on the basis of conversations with responsible agencies (when available). Links to 

information about the programs that have been implemented 

are also provided under “Source.”

References Cited

Abbene, I.J., 2010, Shallow groundwater quality in the Village 

of Patchogue, Suffolk County, New York: U.S. Geological Survey Scientific Investigations Report 2010–5132, 

19 p., accessed June 6, 2017, at http://pubs.usgs.gov/

sir/2010/5132/.

Bricelj, V.M., 2009, The Hard Clam Research Initiative—

Factors controlling Mercenaria mercenaria populations in 

South Shore bays of Long Island, NY: Sea Grant New York 

NYSGI–T–09–001, 7 p., accessed July 3, 2017, at 

http://www.seagrant.sunysb.edu/hclam/pdfs/HardClamsExecSum_Conclusions09.pdf.

Cartwright, R.A., and Schubert, C.E., 2016, South Shore 

Estuary Reserve total maximum daily load monitoring: U.S. Geological Survey dataset, accessed July 3, 

2017, at https://www.sciencebase.gov/catalog/

item/560155fde4b03bc34f544447.

CBS New York, 2013, Federal Sandy aid to fund dredging, 

beach replenishment on Long Island’s South Shore: CBS 

Broadcasting, February 4, 2013, accessed June 21, 2017, 

at http://newyork.cbslocal.com/2013/02/04/federal-sandyaid-to-fund-dredging-beach-replenishment-on-long-islandssouth-shore/.

Makarewicz, J.C., and Lewis, T.W., 2000, Nutrient and sediment loss from Oneida Lake tributaries—The South Shore 

tributaries: State University of New York—The College at 

Brockport, Studies on Water Resources of New York State 

and the Great Lakes, Technical Reports, paper 84, 54 p., 

accessed July 3, 2017, at http://digitalcommons.brockport.

edu/tech_rep/84.

Scientific Investigations Report 2013–5171, 65 p., accessed 

July 3, 2017, at http://dx.doi.org/10.3133/sir20135171.

New York State Department of Environmental Conservation, 

2008, Carmans River biological assessment: New York 

State Department of Environmental Conservation biological 

stream assessment, 46 p.

New York State Department of Environmental Conservation, 

2016, Great South Bay/Fire Island Inlet watershed: New 

York State Department of Environmental Conservation 

water-quality assessment, 71 p., accessed June 21, 2017, at 

http://www.dec.ny.gov/docs/water_pdf/wiatllisgsbfii.pdf.

Stephenson, L.B., 2009, Eelgrass management plan for the 

Peconic Estuary—Peconic Estuary Program: Peconic 

Estuary Program, 92 p., accessed January 19, 2018, at 

https://www.peconicestuary.org/wp-content/

uploads/2017/06/EelgrassManagementPlanforthePec.pdf.

Stony Brook University School of Marine and Atmospheric Sciences, 2016, Sea conditions at Shinnecock 

Inlet: LIShore web page, accessed December 20, 2016, at 

http://www.lishore.org/shinnecock/latest.php.

Stony Brook University School of Marine and Atmospheric 

Sciences, 2017, Sea conditions at Shinnecock Inlet: LIShore 

web page, accessed July 3, 2017, at http://www.lishore.org/

shinnecock/latest.php.

U.S. Army Corps of Engineers New York District, 2004, 

Atlantic coast of Long Island, Fire Island Inlet to Montauk Point, New York—Reformulation study—Submerged 

aquatic vegetation (SAV) bed characterization: U.S. Army 

Corps of Engineers final report, 83 p. plus appendixes.

U.S. Geological Survey, 1999, Simulation of the effects of 

development of the ground-water flow system of Long 

Island, New York: U.S. Geological Survey Water-Resources 

Investigations Report 98–4069, 57 p. [Also available at 

https://pubs.er.usgs.gov/publication/wri984069.]
72 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 1–1. Recommendations presented in the 2000 South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy and their current status based on stakeholder input for physical constituents, Long Island, New York. [Table corresponds to table 6–3 of the 2000 Coordinated Water Resources Monitoring Strategy (CWRMS). Status denoted as “unknown” indicates that information was not provided that shows whether or not a recommendation was implemented. Reserve, South Shore Estuary Reserve; USGS, U.S. Geological Survey; NWS, National Weather Service; NYSDEC, New York State Department of Environmental Conservation; NPS, National Park Service; USACE, U.S. Army Corps of Engineers; CDM, CDM Smith Consultants; --, not available] Recommendations Affects Status Source Continue streamgaging at nine sites in Reserve Watershed USGS Done -- Consider additional streamgage locations at Patchogue River and a site in eastern Suffolk County that flows to the Reserve USGS Not done -- Measure light transmission through the water column of estuary embayments using transmissiometer Town of Hempstead, Suffolk County Partially done -- Add Secchi disk transparency measurements to all nearshore sampling sites NYSDEC, citizen monitoring, NPS Unknown -- Install a permanent weather monitoring station at Shinnecock Inlet USGS, NWS, USACE Done Stony Brook University School of Marine and Atmospheric Sciences (2016); http://www.lishore.org/shinnecock/lat- est.htm Discuss the need for a third weather monitoring station at Fire Island Inlet USGS, NWS, USACE Unknown -- Discuss the need for additional tide stage monitoring stations to meet objec- tives for coastal flood warning system USGS, USACE Done Stony Brook University School of Marine and Atmospheric Sciences (2017); http://www.lishore.org/ Add continual measurements of temperature and salinity at hydrodynamic data collection stations USACE Done U.S. Army Corps of Engineers New York District (2004); http://www.nan.usace. army.mil/Portals/37/docs/civilworks/ projects/ny/coast/fimp/FIMP2.pdf Aerial photographs of barrier islands to track changes in inlet topography USACE Done -- Support development of hydrodynamic model of Reserve embayments (LIShore or equivalent) Technical agencies, universities, potential contractors Done -- Complete three-dimensional groundwater flow model for entire Reserve region using refined grid size USGS, Suffolk County, CDM, universities, and potential contractors Done U.S. Geological Survey (1999); https://pubs.usgs.gov/wri/wri984069/ pdf/wrir_98-4069.pdf Build in capability to monitor turbidity and chlorophyll a at hydrodynamic 

data collection stations

USACE or other potential contractors Done --
Appendix 1 73

Table 1–2. Recommendations presented in the 2000 South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy and their current status based on stakeholder input for chemical constituents for tributary monitoring, Long Island, New York.[Table corresponds to table 6–4 of the 2000 Coordinated Water Resources Monitoring Strategy (CWRMS). N, nitrogen; SRP, soluble reactive phosphorus; --, not available]

Objective Sampling locations Constituent list Frequency Status Source

Annual loading of nutrients 

and sediment. Relative concentration of N species. Priority areas for remedial measures

Carmans River (top priority), Carlls 

River, East Meadow Brook, Patchogue River, Connetquot Brook, Swan River, Sampawans Creek, Massapequa Creek, Bellmore Creek

SS, TKN, NH3, NO3, 

TP, SRP, SAL, WT, DO, pH

Biweekly to monthly, 

plus additional samples during high flows

Partially 

done

New York State Department of 

Environmental Conservation (2008);http://www.dec.ny.gov/docs/water_pdf/sbucarmans08.pdf 

Use impairment Swan River, Sampawams Creek, 

Beaverdam Creek, Neguntatouge Creek, Carmans River, Carlls River, East Meadow Brook, Patchogue River, Connetquot Brook

SAL, WT, DO, pH Monthly: May, June, and 

October biweekly: July, August, and September

Done New York State Department of 

Environmental Conservation (2016); http://www.dec.ny.gov/docs/water_pdf/wiatllisgsbfii.pdf

Effectiveness of stormwater 

management practices

None determined SS, TKN, TP, FIB Storm sampling, before 

and after improvements

Not done --
74 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 1–3. Recommendations presented in the 2000 South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy and their current status based on stakeholder input for analytical constituents for tributary monitoring, Long Island, New York. [Table corresponds to table 6–5 of the 2000 Coordinated Water Resources Monitoring Strategy (CWRMS). Status denoted as “unknown” indicates that information was not provided that shows whether or not a recommendation was implemented. N, nitrogen; P, phosphorus; mg/L, milligram per liter; --, not available] Constituent Depths Limit of detection Rationale/notes Status Source Water temperature, dissolved oxygen, pH, specific conductance Mid-depth, midchannel Field meter General habitat quality and water quality surveillance Partially done Makarewicz and Lewis (2000); http://digitalcommons.brockport.edu/tech_rep/84 Total Kjeldahl N (TKN) Flow-weighted composite sample 0.03 mg/L General habitat quality, water quality surveillance, salinity Unknown -- Nitrite + nitrate N Flow-weighted composite sample 0.0002 mg/L (as N) Concentration and load Done Mullaney and Schwarz (2013); http://dx.doi.org/10.3133/sir20135171 Total P Flow-weighted composite sample 0.001 mg/L Concentration and load Done Makarewicz and Lewis (2000); http://digitalcommons.brockport.edu/tech_rep/84 Soluble reactive P (SRP) Flow-weighted composite sample 0.0006 mg/L Concentration and load Not done -- Total suspended solids (TSS) Flow-weighted composite sample 2 mg/L Concentration and load Unknown --
Appendix 1 75

Table 1–4. Recommendations presented in the 2000 South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy and their current status based on stakeholder input for chemical constituents for embayment monitoring, Long Island, New York.[Table corresponds to table 6–6 of the 2000 Coordinated Water Resources Monitoring Strategy (CWRMS). Status denoted as “unknown” indicates that information was not provided that shows whether or not a recommendation was implemented. DKN, dissolved Kjeldahl nitrogen; P, phosphorus; m, meter; °C, degree Celsius; %, percent; ppt, part per thousand; mg/L, milligram per liter; NTU, nephelometric turbidity unit; N, nitrogen; SAV, submerged aquatic vegetation; --, not available]

Constituent Depths Stations Limit of detection Rationale/notes Status Source

Water temperature 0.5 m below surface, 

0.5 m above bottom

All Field meter (0.1°C) Assess water temperature, 

stratification

Not done --

Salinity 0.5 m below surface, 

0.5 m above bottom

All Field meter (specific 

conductance, 10% of scale)

Assess water temperature, 

stratification

Partially 

done

Cartwright and Schubert (2016); 

https://www.sciencebase.gov/catalog/item/560155fde4b03bc34f544447

Discrete sample at 0.5 m 

(Nisken bottle)

Every five 

stations

Induction salinometer 

(0.1 ppt)

Comparability with historical 

data, quality control for meters

Unknown --

Chlorophyll a (total and 

< 10 micrometers)

Discrete sample at

0.5 m (Nisken bottle)

All Fluorometric 

(1 mg/L)

Primary production, 

phytoplankton community composition.

Done Cartwright and Schubert (2016);

https://www.sciencebase.gov/catalog/item/560155fde4b03bc34f544447

Total Kjeldahl N (TKN) Discrete sample at

0.5 m (Nisken bottle)

All .03 mg/L Total N and fractions (nutrient 

status plus brown tide conditions), SAV criteria

Not done --

DKN Discrete sample at

0.5 m (Nisken bottle)

All .026 mg/L Total N and fractions, SAV 

criteria

Not done --

Urea Discrete sample at

0.5 m (Nisken bottle)

All .05 mg/L Total N and fractions, SAV 

criteria

Not done --

Ammonia Discrete sample at

0.5 m (Nisken bottle)

All .004 mg/L Total N and fractions, SAV 

criteria

Partially 

done

Abbene (2010); http://pubs.usgs.gov/

sir/2010/5132/

Nitrite + nitrate Discrete sample at

0.5 m (Nisken bottle)

All .0002 mg/L Total N and fractions, SAV 

criteria

Done Cartwright and Schubert (2016); 

https://www.sciencebase.gov/catalog/item/560155fde4b03bc34f544447

Total P Discrete sample at

0.5 m (Nisken bottle)

All .001 mg/L SAV criteria, nutrient status, 

particulate and dissolved partitioning

Unknown --

Soluble reactive P .0006 mg/L Not done --Total suspended solids 

(TSS)

Discrete sample at 0.5 m 

(Nisken bottle)

All 2 mg/L Light penetration, SAV 

criteria

Unknown --

Turbidity Discrete sample at 0.5 m 

(Nisken bottle)

All .5 NTU Light penetration, correlation Unknown Abbene (2010); http://pubs.usgs.gov/

sir/2010/5132/

Total organic carbon Discrete sample at 0.5 m 

(Nisken bottle)

All .1 mg/L Trophic status, impacts 

of treated wastewater discharge

Unknown --
76 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 1–5. Recommendations presented in the 2000 South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy and their current status based on stakeholder input for changes to existing monitoring, Long Island, New York. [Table corresponds to table 6–7 of the 2000 Coordinated Water Resources Monitoring Strategy (CWRMS). NYSDEC, New York State Department of Environmental Conservation; TSS, total suspended solids; TKN, total Kjeldahl nitrogen; P, phosphorus; BOD, biological oxygen demand; --, not available] Agency and program Recommended changes to monitoring program Status Suffolk County Health Department Retain existing monitoring network, discuss with Town of Hempstead the logistics of adding four stations in South Oyster Bay Not done Standardize monitoring frequency to biweekly, year-round, with winter monitoring as conditions allow Add phytoplankton, zooplankton, and macroinvertebrates at limited number of stations Add turbidity Eliminate (from tier 1) silica, dissolved organic carbon Town of Hempstead Water Quality Monitoring Program Retain existing monitoring network, discuss with Suffolk County the logistics of adding four stations in South Oyster Bay Not done Standardize monitoring frequency to biweekly, year-round, with winter monitoring as conditions allow Add TSS Add phytoplankton, zooplankton, and macroinvertebrates at limited number of stations Add turbidity Add total organic carbon Add TKN (total plus dissolved fractions) Add size fractionation of chlorophyll analysis Add soluble reactive P Eliminate (from tier 1) BOD and particulate organic material NYSDEC (shellfish sanitation) Add Secchi disk transparency Not done Add turbidity (minimum) and (or) TSS (preferable) Not done Add salinity Partially done
Appendix 1 77

Table 1–6. Recommendations presented in the 2000 South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy and their current status based on stakeholder input for biological constituents for tributary monitoring, Long Island, New York.[Table corresponds to table 6–8 of the 2000 Coordinated Water Resources Monitoring Strategy (CWRMS). EPT, Ephemeroptera, Plecoptera, and Trichoptera]

Monitoring constituents Frequency Comments Status

Macroinvertebrate community: Hilsenhoff Biotic Index, EPT 

richness, species richness, species dominance, species diversity

Rotating, once every three years in each stream, 

during summer (June–September)

Multiplate deployment in depositional 

areas; kick screens in upstream reaches

Not done

Fecal coliform bacteria Monthly, additional samples during high flows Additional monitoring included as tier 2 Not done
78 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 1–7. Recommendations presented in the 2000 South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy and their current status based on stakeholder input for biological constituents for embayment monitoring, Long Island, New York. [Table corresponds to table 6–9 of the 2000 Coordinated Water Resources Monitoring Strategy (CWRMS).Status denoted as “unknown” indicates that information was not provided that shows whether or not a recommendation was implemented; --, not available] Constituent Location Recommended frequency Objective Status Source Brown tide 

(Aureococcus anophagefferens)

Shinnecock (mid-bay), 

Great South Bay, Oyster Bay (coves and inlets) (see table 6–2 of 2000 CWRMS)

Biweekly Bloom monitoring Done --

Hard clam population 

and harvest (landings)

Estuary wide Annual

(town leadership)

Trends and use 

attainment

Done Bricelj (2009); http://www.seagrant.sunysb.edu/hclam/

pdfs/HardClams-ExecSum_Conclusions09.pdf

Fecal coliform bacteria At all limnological sites, plus 

shellfish sanitation sites

Per regulations for 

certified, uncertified,and conditional shellfish areas

Public health Done --

Enterococcus At bathing beach sites Five samples/month 

during recreational season

Public health, correlation 

between new and existing indicators

Not done --

Phytoplankton 

(numbers and biovolume ofmajor taxa)

Selected stations 

(approximately 10)

Biweekly Community structure, 

annual succession

Partially 

done

--

Zooplankton (numbers 

and biomass of major taxa)

Selected stations 

(approximately 10)

Biweekly Community structure, 

annual succession

Unknown --

Macroinvertebrates 

(benthos)

Selected stations (6–10) Four times annually Biomass and diversity Not done --

Macroalgae beds Estuary wide Annual visual surveys

in August

Trends, attainment of 

ecosystem goals

Partially 

done

Stephenson (2009); https://www.peconicestuary.

org/wp-content/uploads/2017/06/EelgrassManagementPlanforthePec.pdf

Submerged aquatic 

vegetation (SAV)

Estuary-wide subtidal zone A Annual aerial survey, 

field verified every3 years

Develop data base for 

trend analysis

Unknown --
Appendix 1 79

Table 1–8. Recommendations presented in the 2000 South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy and their current status based on stakeholder input for human-induced constituents, Long Island, New York.[Table corresponds to table 6–10 of the 2000 Coordinated Water Resources Monitoring Strategy (CWRMS). Status denoted as “unknown” indicates that information was not provided that shows whether or not a recommendation was implemented. NYSDEC, New York State Department of Environmental Conservation; USACE, U.S. Army Corps of Engineers; Cornell CE, Cornell Cooperative Extension; --, not available]

Program Constituents to monitor Primary data source Frequency Status Source

Tributary and 

watershed

Impervious cover, by 

subwatershed

County planning agencies Annual data compilation Unknown --

Wetland areas disturbed 

and filled

NYSDEC and USACE Annual data compilation Unknown --

Detailed land-use data Town and county planning 

agencies

Annual data compilation Partially 

done

--

Stream restoration 

activities

Soil and Water Conservation 

Districts, town engineers, and Department of Public Works

Annual data compilation Partially 

done

--

Estuary Hard clam harvest and 

seeding

Towns, NYSDEC, Cornell 

CE

Annual Done --

Dredging USACE Every three years Done CBS New York (2013); http://newyork.cbslocal.

com/2013/02/04/federal-sandy-aid-to-fund-dredgingbeach-replenishment-on-long-islands-south-shore/

Volume and quality of 

effluent

NYSDEC Annual compilation of discharge 

monitoring reports

Unknown --

Ocean Inlet dredging and 

beach erosion control measures

USACE Every five years Unknown --

Appendix 2 81

Appendix 2. New York State Department of Environmental Conservation 303(d) 

List of Impaired Waters
82 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 2–1.

Waterbodies of the South Shore Estuary Reserve included in the 2014 New York State Department of Environmental Conservation 303(d) List of Impaired Waters along 

with their statuses and associated monitoring programs.[NYSDEC, New York State Department of Environmental Conservation; RIBS, Rotating Integrated Basin Studies; PCB, polychlorinated biphenyl; DO, dissolved oxygen; VOC, volatile organic compound; USGS, U.S. Geological Survey; ToH, Town of Hempstead; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; WQ, water quality; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; HSC, horseshoe crab; NYS, New York State; SCDHS, Suffolk County Department of Health Services; TNC, The Nature Conservancy; GSBP, Great South Bay Project; GSB, Great South Bay; WQM, water quality monitoring; TMDL, total maximum daily load; WWTP, wastewater treatment plant]

Waterbody 303(d) Class Pollution type Reserve monitoring programs Status Pollution source

Hempstead Bay

Hempstead Bay SA Nutrients (Nitrogen), Pathogens, PCBs, Algal 

Growth, Ammonia, oxygen demand

USGS Estuary Monitoring, ToH Bay 

Study, SoMAS News 12 WQ Index WQ Index, SoMAS Sediment Quality

Impaired Water Requiring a TMDL MUNICIPAL (Bay Park, Oth- ers), Urban/Storm Runoff

Grant Park Pond

C Nutrients (Phosphorus), Pathogens, PCBs, 

Sediment/Silt, Algal Growth, Oxygen Demand, pathogens

None Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, Other Sanitary Disch, TOX/

CONTAM. SEDIMENT

Smith Pond

C PESTICIDES (chlordane), Aquatic Invasive 

Species, Nutrients (phosphorus), Silt/Sediment, Low DO/Oxygen Demand

ToH Tributaries, NYSDEC RIBS Impaired Water Requiring a TMDL TOX/CONTAM SED, Habitat Alteration, Urban/Storm 

Runoff

Hempstead Lake

C NUTRIENTS (phosphorus), oxygen demand ToH Tributaries, NYSDEC RIBS Impaired Water Requiring a TMDL URBAN/STORM RUNOFF

Milburn/Parsonage 

Creeks

C UNKNOWN POLLUTANT (Biological Impact), PESTICIDES (chlordane), Nutrients 

(Phosphorus), Algal/Plant Growth, Silt/Sediment, oxygen demand

NYSDEC RIBS Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, TOX/CONTAM. SEDIMENT

Freeport Reservoir/East 

Meadow Pond

A Nutrients, Pesticides (chlordane), Sediment/

silt, Algal Growth, Oxygen Demand

NYSDEC RIBS Impaired Water Requiring a TMDL Urban/Storm Runoff, TOX/ CONTAM. SEDIMENT

Camaans Pond

C Phosphorus, Pathogens, Sediment/silt, Algal 

Growth, Oxygen demand

NYSDEC RIBS Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, Other (waterfowl)

Hog Island Channel SB PATHOGENS, ALGAL/PLANT GROWTH 

(Ulva/sea lettuce), NUTRIENTS (nitrogen), Priority Organics (PCBs/migratory fish), Oxygen Demand

USGS Estuary Monitoring, ToH Bay 

Study, SoMAS Sediment Quality

Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, MUNICIPAL (Bay Park, 

other)

Freeport Reservoir/East 

Meadow Pond

SA PATHOGENS, Priority Organics (PCBs/

migratory fish), Nutrients (nitrogen), Algal/Plant Growth

ToH Bay Study, ToH Tributaries, SoMAS Sediment Quality Impaired Water Requir- ing a TMDL URBAN/STORM RUNOFF, Other Source (migratory fish 

species), Municipal, Habitat Alteration 

Tidal tributary to Hempstead Bay SC Algal Growth, NUTRIENTS (Nitrogen), Pathogens, Oxygen Demand, PCBs, Ammonia ToH Bay Study, SoMAS Sediment Quality, ToH Tributaries Impaired Water Requir- ing a TMDL MUNICIPAL (Bay Park, Oth- ers), Urban/Storm Runoff, Other Source (migratory fish 

species)

East Bay SA Pathogens, PCBs, ToH Bay Study, SoMAS Sediment 

Qaulity,USGS Surface Water Monitoring

Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, Other Source (migratory 

species)
Appendix 2 83

Table 2–1. Waterbodies of the South Shore Estuary Reserve included in the 2014 New York State Department of Environmental Conservation 303(d) List of Impaired Waters along with their statuses and associated monitoring programs.—Continued[NYSDEC, New York State Department of Environmental Conservation; RIBS, Rotating Integrated Basin Studies; PCB, polychlorinated biphenyl; DO, dissolved oxygen; VOC, volatile organic compound; USGS, U.S. Geological Survey; ToH, Town of Hempstead; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; WQ, water quality; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; HSC, horseshoe crab; NYS, New York State; SCDHS, Suffolk County Department of Health Services; TNC, The Nature Conservancy; GSBP, Great South Bay Project; GSB, Great South Bay; WQM, water quality monitoring; TMDL, total maximum daily load; WWTP, wastewater treatment plant]

Waterbody 303(d) Class Pollution type Reserve monitoring programs Status Pollution source

Hempstead Bay—Continued

Tributary (fresh) to East 

Bay

C Silt/Sediment, Phosphorus ToH Tributaries, SoMAS Sediment 

Quality

Impaired Water Requiring a TMDL URBAN/STORM RUNOFF

Woodmere Channel SA ALGAL/PLANT GROWTH (Ulva/sea lettuce), NUTRIENTS (Nitrogen), PATHOGENS, Oxygen Demand/Low DO, Priority 

Organics, Ammonia

None Impaired Water Requiring a TMDL MUNICIPAL (Bay Park, Oth- ers), Urban/Storm Runoff

Reynolds Channel, East SA ALGALGROWTH, PATHOGENS, NUTRIENTS (Nitrogen), PCBs ToH Bay Study, SoMAS sediment quality Impaired Water Requir- ing a TMDL URBAN/STORM RUNOFF, HABITAT ALTERATION, 

MUNICIPAL (Bay Park, other)

Reynolds Channel, West SB ALGAL GROWTH (Ulva/sea lettuce), NUTRIENTS (Nitrogen), Pathogens, Priority 

Organics (PCBs/migratory fish), Ammonia

ToH Bay Study, ToH Vertical Profiles, 

USGS Estuary Monitoring, SoMAS sediment quality 

Impaired Water Requiring a TMDL HABITAT ALTERATION, MUNICIPAL (Bay Park, 

other), Urban/Storm Runoff, Other Source (migratory fish species)

East Rockaway Inlet SA Pathogens ToH Bay Study, CERCOM HSC Inventory Impaired Water Requir- ing a TMDL URBAN/STORM RUNOFF, Habitat Alteration, MUNICIPAL (Bay Park, other), Other 

Source (migratory fish species), Municipal

South Oyster Bay

South Oyster Bay SA Pathogens, PCBs ToH Bay Study, SoMASsediment quality, NYS Department of Health WQ, 

SoMAS News 12 WQ Index WQ index, CERCOM HSC

Impaired Water Requiring a TMDL URBAN/STORM RUNOFF

Tidal tributaries to 

South Oyster Bay

SC PATHOGENS, Algal/Plant Growth ToH Bay Study, NYS Department of 

Health WQ, SoMAS Sediment

Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, Other/Non-Permitted Sanitary 

Discharge

Wantagh/Seamans Pond A PESTICIDES (chlordane), Aquatic Invasive 

Species

None Impaired Water Requiring a TMDL Habitat Alteration, TOX/CON- TAMINATED SED

Massapequa Reservoir A Nutrients, Pathogens, Pesticide (Chlordane), 

Sediment/Silt, Algal Growth

NYSDEC RIBS Impaired Water Requiring a TMDL Urban/Storm Runoff, TOXIC/ CONTAMINATED SEDIMENT
84 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 2–1.

Waterbodies of the South Shore Estuary Reserve included in the 2014 New York State Department of Environmental Conservation 303(d) List of Impaired Waters along 

with their statuses and associated monitoring programs.—Continued[NYSDEC, New York State Department of Environmental Conservation; RIBS, Rotating Integrated Basin Studies; PCB, polychlorinated biphenyl; DO, dissolved oxygen; VOC, volatile organic compound; USGS, U.S. Geological Survey; ToH, Town of Hempstead; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; WQ, water quality; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; HSC, horseshoe crab; NYS, New York State; SCDHS, Suffolk County Department of Health Services; TNC, The Nature Conservancy; GSBP, Great South Bay Project; GSB, Great South Bay; WQM, water quality monitoring; TMDL, total maximum daily load; WWTP, wastewater treatment plant]

Waterbody 303(d) Class Pollution type Reserve monitoring programs Status Pollution source

South Oyster Bay—Continued

Massapequa Creek, 

Upper, and tributary

C Nutrients (phosphorus), Pathogens, Sediment/silt, VOCs, Cadmium, Algal Growth, 

Oxygen Demand

USGS Surface Water Monitoring Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, OTHER/NON-PERMITTED 

SANITARY DISCHARGE, Other Source (waterfowl), Landfill/Land Disposal

Seafords/Seamans 

Creeks, and tidal tributary

SC Pathogens, Algal Growth None Impaired Water Requiring a TMDL URBAN/STORM RUNOF

Great South Bay

Great South Bay, West SA ALGAL/PLANT GROWTH (BROWN 

TIDE), NUTRIENTS (NITROGEN), Pathogens, PCBs, Oxygen Demand

USGS Estuary Monitoring, NYS 

Department of Health WQ, SoMAS LIShore, SoMAS Great South Bay project, SCDHS WQ, SCDHS Beach, CERCOM HSC

Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, Municipal Discharges, ONSITE/SEPTIC SYST

Great South Bay, 

Middle

SA ALGAL/PLANT GROWTH (BROWN 

TIDE), NUTRIENTS (NITROGEN), Pathogens, PCBs, Oxygen Demand

TNC DO, SCDHS WQ Monitoring, 

NYS Department of Health WQ, CERCOM Water Quality, CERCOM Plankton, SoMAS Great South Bay project, USGS Estuary Monitoring, SCDHS WQ, SoMAS News 12 WQ Index

Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, Onsite/Septic Systems, Municipal Discharges

Great South Bay, East SA ALGAL/PLANT GROWTH (brown tide), 

NUTRIENTS (nitrogen), Pathogens, Priority Organics (PCBs/migratory fish), Low DO/Oxygen Demand

TNC DO, NYS Department of Health 

WQ, CERCOM Water Quality, CERCOM Plankton, SoMAS Great South Bay project, SoMAS Great South Bay Project, USGS Estuary Monitoring, SCDHS WQ, SoMAS LIShore

Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, Municipal Discharges, 

ON-SITE/SEPTIC SYST, Other Source (migratory fish species)

Patchogue Bay SA PATHOGENS, Ammonia, Chlorine, Algal 

Growth (brown tide), Nutrients, Priority Organics (PCBs/migratory fish)

SCDHS WQ, SoMAS GSBP Impaired Water, TMDL 

Completed

MUNICIPAL DISCHARGES 

(Patchogue WWTP), URBAN/STORM RUNOFF, On-Site/Septic Syst

Great Cove SA Pathogens, Nutrients, oxygen demand, PCBs SCDHS WQM, SoMAS GSBP, SoMAS News 12 WQ Index Impaired Water, TMDL Completed URBAN/STORM RUNOFF, Onsite/Septic Systems
Appendix 2 85

Table 2–1. Waterbodies of the South Shore Estuary Reserve included in the 2014 New York State Department of Environmental Conservation 303(d) List of Impaired Waters along with their statuses and associated monitoring programs.—Continued[NYSDEC, New York State Department of Environmental Conservation; RIBS, Rotating Integrated Basin Studies; PCB, polychlorinated biphenyl; DO, dissolved oxygen; VOC, volatile organic compound; USGS, U.S. Geological Survey; ToH, Town of Hempstead; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; WQ, water quality; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; HSC, horseshoe crab; NYS, New York State; SCDHS, Suffolk County Department of Health Services; TNC, The Nature Conservancy; GSBP, Great South Bay Project; GSB, Great South Bay; WQM, water quality monitoring; TMDL, total maximum daily load; WWTP, wastewater treatment plant]

Waterbody 303(d) Class Pollution type Reserve monitoring programs Status Pollution source

Great South Bay—Continued

Bellport Bay SA PATHOGENS, Algal Growth (brown tide), 

Nutrients, PCBs

USGS Estuary Monitoring, SCDHS 

WQM, SoMAS GSBP, SoMAS, News 12 WQ Index

Impaired Water, TMDL 

Completed

Urban/Storm Runoff, onsite 

septic system

Sampawams Creek, 

Upper and tributary

C UNKNOWN POLLUTANTS (biological 

impacts), Nutrients, Pathogens, oxygen demand

USGS Surface Water Quality Monitoring Impaired Water Requir- ing a TMDL URBAN/STORM RUNOFF

Lake Capri C Chlordane, Cadmium, Phosphorus None Impaired Water Requiring a TMDL TOXIC/CONTAMINATED SEDIMENT

Nicoll Bay SA Pathogens, Nutrients, oxygen demand, PCBs TNC DO, SCDHS WQ Impaired Water, TMDL 

Completed

Urban/Storm Runoff, onsite 

septic system

Penataquit Creek C UNKNOWN POLLUTANTS (biological 

impacts), Nutrients (phosphorus), Low DO/Oxygen Demand, Pathogens

USGS Surface Water Quality Monitoring Impaired Water Requir- ing a TMDL Urban/Storm Runoff, onsite septic system

Awixa Creek C UNKNOWN POLLUTANTS (biological 

impacts), Nutrients (phosphorus), Low DO/Oxygen Demand, Pathogens

None Impaired Water Requiring a TMDL Urban/Storm Runoff, onsite septic system, Hydrologic 

Alteration

Orowoc Creek C UNKNOWN POLLUTANTS (biological 

impacts), Nutrients (phosphorus), Low DO/Oxygen Demand, Water Level/Flow, Pathogens

None Impaired Water Requiring a TMDL Urban/Storm Runoff, onsite septic system

Champlin Creek, upper, 

and tributary

C(TS) Thermal Changes, UNKNOWN POLLUTANTS (biological impacts), Nutrients 

(phosphorus), Low DO/Oxygen Demand, Pathogens

USGS Surface Water Quality Monitoring Impaired Water Requir- ing a TMDL Urban/Storm Runoff, onsite septic system

Canaan Lake B(T) Aquatic Invasive Species (milfoil, fanwort), 

Algal Growth (native), Nutrients (phosporus), Silt/Sediment

NYSDEC RIBS Impaired Water Requiring a TMDL Habitat Alteration, Urban/Storm Runoff
86 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 2–1.

Waterbodies of the South Shore Estuary Reserve included in the 2014 New York State Department of Environmental Conservation 303(d) List of Impaired Waters along 

with their statuses and associated monitoring programs.—Continued[NYSDEC, New York State Department of Environmental Conservation; RIBS, Rotating Integrated Basin Studies; PCB, polychlorinated biphenyl; DO, dissolved oxygen; VOC, volatile organic compound; USGS, U.S. Geological Survey; ToH, Town of Hempstead; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; WQ, water quality; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; HSC, horseshoe crab; NYS, New York State; SCDHS, Suffolk County Department of Health Services; TNC, The Nature Conservancy; GSBP, Great South Bay Project; GSB, Great South Bay; WQM, water quality monitoring; TMDL, total maximum daily load; WWTP, wastewater treatment plant]

Waterbody 303(d) Class Pollution type Reserve monitoring programs Status Pollution source

Moriches Bay

Moriches Bay, East SA ALGAL/PLANT GROWTH (Brown Tide), 

Pathogens, NUTRIENTS (nitrogen), Low DO/Oxygen Demand

SCDHS WQ, CERCOM HSC Impaired Water Requiring a TMDL OTHER SOURCE (boat pol- lution), URBAN/STORM 

RUNOFF, AGRICULTURE, ON-SITE/SEPTIC SYST

Moriches Bay, West SA ALGAL/PLANT GROWTH (Brown Tide), 

Pathogens, NUTRIENTS (nitrogen), Low DO/Oxygen Demand

SCDHS WQ, SoMAS GSB Impaired Water Requiring a TMDL OTHER SOURCE (boat pol- lution), URBAN/STORM 

RUNOFF, AGRICULTURE, ON-SITE/SEPTIC SYST

Tidal NYSDEC RIBS to 

West Moriches Bay

SC Pathogens, oxygen demand SCDHS WQ Impaired Water Requiring a TMDL Urban/Storm Runoff, agriculture

West Mill Pond

C Nutrients, Pathogens, Sediment/silt, Oxygen 

Demand

None Impaired Water Requiring a TMDL AGRICULTURE (duck farms), Urban/Storm Runoff, Other 

Non-Permitted Sanitary Disch

Forge River, Lower and 

Cove

SA Pathogens SCDHS WQM, SoMAS News 12 WQ 

Index, 

Impaired Water Requiring a TMDL URBAN/STORM RUN- OFF, Agriculture, OTHER 

SOURCE (waterfowl/wildlife) 

Narrow Bay SA Pathogens SCDHS WQ, CERCOM HSC, USGS 

Surface Water, CERCOM HSC

Impaired Water, TMDL 

Completed

URBAN/STORM RUNOFF, Agriculture, OTHER 

SOURCE (waterfowl/wildlife) 

Ogden Pond SA Pathogens SCDHS Impaired Water, TMDL 

Completed

URBAN/STORM RUNOFF, Agriculture, OTHER 

SOURCE (waterfowl/wildlife) 

Beaverdam Creek and 

tributary

C(TS) Nutrients, Unknown Toxicity, Ammonia, 

Oxygen Demand

USGS Surface Water Quality Monitoring, SCDHS WQM Waterbodies for which TMDL Development 

May be Deferred (Requiring Verification of Cause/Pollutant/Source)

URBAN/STORM RUNOFF
Appendix 2 87

Table 2–1. Waterbodies of the South Shore Estuary Reserve included in the 2014 New York State Department of Environmental Conservation 303(d) List of Impaired Waters along with their statuses and associated monitoring programs.—Continued[NYSDEC, New York State Department of Environmental Conservation; RIBS, Rotating Integrated Basin Studies; PCB, polychlorinated biphenyl; DO, dissolved oxygen; VOC, volatile organic compound; USGS, U.S. Geological Survey; ToH, Town of Hempstead; SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; WQ, water quality; CERCOM, Center for Environmental Research and Coastal Oceans Monitoring; HSC, horseshoe crab; NYS, New York State; SCDHS, Suffolk County Department of Health Services; TNC, The Nature Conservancy; GSBP, Great South Bay Project; GSB, Great South Bay; WQM, water quality monitoring; TMDL, total maximum daily load; WWTP, wastewater treatment plant]

Waterbody 303(d) Class Pollution type Reserve monitoring programs Status Pollution source

Shinnecock Bay

Quantuck Bay SA ALGAL/PLANT GROWTH (Brown Tide), 

PATHOGENS, NUTRIENTS (nitrogen), Low DO/Oxygen Demand

SCDHS WQ, SoMAS News 12 WQ 

Index

Impaired Water Requiring a TMDL OTHER SOURCE (boat pol- lution), URBAN/STORM 

RUNOFF, ON-SITE/SEPTIC SYST

Shinnecock Bay and 

Inlet

SA ALGAL/PLANT GROWTH (brown/rust 

tide), NUTRIENTS (nitrogen), Pathogens, Priority Organics (PCBs/migratory fish), Low DO/Oxygen Demand

SCDHS WQ, SoMAS News 12 WQ 

Index, SoMAS LIShore

Impaired Water Requiring a TMDL URBAN/STORM RUNOFF, Municipal Discharges, ONSITE/SEPTIC SYST, OTHER 

SOURCE (migratory fishspecies)

Weesuck Creek SA Pathogens None Impaired Water, TMDL 

Completed

URBAN/STORM RUNOFF, Agriculture, OTHER 

SOURCE (waterfowl/wildlife) 

Phillips Creek, Lower, 

and tidal tributary

SA Pathogens None Impaired Water Requiring a TMDL URBAN/STORM RUN- OFF, Agriculture, OTHER 

SOURCE (waterfowl/wildlife) 

Quogue Canal SA Pathogens None Impaired Water Requiring a TMDL URBAN/STORM RUN- OFF, Agriculture, OTHER 

SOURCE (waterfowl/wildlife) 

Appendix 3 89

Appendix 3. Expanded List of Management Plans Created or in Progress for 

Resources Within the Long Island South Shore Estuary Reserve, New York
90 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Table 3–1. Management plans developed for water and resources management in the South Shore Estuary Reserve in Long Island, New York, since 2000, with years of publication, cooperating organizations, and funding agencies. [Supplement to table 2. SSER, South Shore Estuary Reserve; CMP, Comprehensive Management Plan; NYSDOS, New York State Department of State; NPS, National Park Service; NYSDEC, New York State Department of Environmental Conservation; NYSERDA, New York State Energy Research and Development Authority; TNC, The Nature Conservancy; GOSR, Governor’s Office of Storm Recovery] Management plan/assessment Management plan abbreviation Year published Reserve waterways Stakeholder Funding agency South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy SSER CWRMS 2000 2000 Entire Reserve NYSDOS NYSDOS South Shore Estuary Reserve Comprehensive Management Plan SSER CMP 2001 Entire Reserve NYSDOS NYSDOS Southampton Marine Resources Protection and Management Plan SH MRPMP 2001 Shinnecock Bay, Moriches Bay Southampton Board of Trustees NYSDOS Town of Southampton Shellfish Feasibility Study SH SFS 2003 Shinnecock Bay, Moriches Bay Southampton Board of Trustees Southampton Board of Trustees SSER CMP Implementation Status Report 2001–03 SSER CMP ISR 2003 2003 Entire Reserve NYSDOS NYSDOS SSER CMP Implementation Status Report 2003–05 SSER CMP ISR 2005 2005 Entire Reserve NYSDOS NYSDOS Green’s Creek and Brown’s River Watershed Management Plan GCBR WMP 2006 Green Creek, Brown Creek Town of Islip NYSDOS, Town of Islip Swan River Watershed Management Plan SR WMP 2007 Swan River Town of Brookhaven NYSDOS, Town of Brookhaven Beaver Dam Creek Watershed Management Plan BDC WMP 2009 Beaverdam Creek Town of Brookhaven NYSDOS, Town of Brookhaven Natural Resources Assessment—Fire Island National Seashore NRA FIIS 2009 Great South Bay, Atlantic Ocean NPS NPS Massapequa Creek Watershed Management and Corridor Restoration Plan MC WMCRP 2009 Massapequa Creek Town of Oyster Bay NYSDOS, Town of Oyster Bay New York State Seagrass Task Force NYS STF 2009 Entire Reserve New York State Seagrass Taskforce NYSDEC South Oyster Bay Hard Clam Population Survey SOB HCPS 2009 South Oyster Bay Town of Oyster Bay NYSDOS, Town of 

Oyster Bay

Town of Oyster Bay SSER Workplan Implementation—Open Space Preservation Plan TOB SSER WIOSPP 2010 South Oyster Bay, Massapequa Creek Town of Oyster Bay NYSDOS, Town of Oyster BayNatural Resources Program NRP 2010 Entire Reserve NYSDOS NYSDOS

SSER CMP Implementation Status Report 

2006–10

SSER CMP ISR 2010 2011 Entire Reserve NYSDOS NYSDOS

New York State ClimAid CLIMAID 2011 Entire Reserve NYSERDA NYSERDA
Appendix 3 91

Table 3–1. Management plans developed for water and resources management in the South Shore Estuary Reserve in Long Island, New York, since 2000, with years of publication, cooperating organizations, and funding agencies.—Continued[Supplement to table 2. SSER, South Shore Estuary Reserve; CMP, Comprehensive Management Plan; NYSDOS, New York State Department of State; NPS, National Park Service; NYSERDA, New York State Energy Research and Development Authority; TNC, The Nature Conservancy; GOSR, Governor’s Office of Storm Recovery]

Management plan/assessment Management plan abbreviation Year published Reserve waterways Stakeholder Funding agency

Great Cove Watershed Management Plan GC WMP 2012 Chaplin Creek, Orowoc Creek, 

Cascade Creek, Penataquit Creek, Awixa Creek, Trues Creek, Lawrence Creek, Thompson’s Creek, Watchogue Creek

Town of Islip NYSDOS, Town of Islip

Forge River Watershed Management Plan FR WMP 2012 Forge River, Moriches Bay Town of Brookhaven NYSDOS, Town of 

Brookhaven

Great South Bay Ecosystem-Based Management 

Plan

GSB EMP 2012 Great South Bay TNC NYSDOS

Carmans River Conservation and Management 

Plan

CR CMP 2013 Carmans River Town of Brookhaven Town of Brookhaven

Long Beach NY Rising Community Reconstruction Plan LB CRP 2014 Hempstead Bay City of Long Beach NY Rising GOSR

Climate Risk Report for Nassau and Suffolk 

Counties

CRR 2014 Entire Reserve NYS RISE Suffolk County, Nassau 

County

Suffolk County Comprehensive Master Plan 2035 SC CMP 2035 2015 Entire Reserve Suffolk County New York Metropolitan Transportation 

Council

Coastal Resiliency and Water Quality in Nassau 

and Suffolk Counties

CRWQ 2015 Entire Reserve NYSDEC, NY RISING NYSDEC, NY Rising 

GOSR

Suffolk County Comprehensive Water Resources 

Management Plan

SC CWRMP 2015 All Suffolk waters in Reserve Suffolk County Suffolk County

Suffolk County Subwatershed Wastewater Plan SC SWP In progress Entire Reserve Suffolk County Suffolk County

Harmful Algal Bloom Action Plan HAB AP In progress Entire Reserve Stony Brook School of 

Marine and Atmospheric Sciences

NYSDOS, New York 

Sea Grant

Long Island Nitrogen Action Plan LINAP In progress Entire Reserve NYSDEC, Long Island Regional Planning Council, 

Suffolk County

NYSDEC

Shinnecock Tribal Lands and Bay Resources 

Management Plan

SHIN RMP In progress Shinnecock Bay, Heady Creek Shinnecock Tribal Nation NYSDOS, Shinnecock 

Tribal Nation

Appendix 4 93

Appendix 4. Members of the Project Advisory Committee for the Long Island 

South Shore Estuary Reserve 2017 Coordinated Water Resources Monitoring 

Strategy
94 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

Table 4–1. Contributors to the meetings at which recommendations were presented for the creation of this document.

[SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; EPA, U.S. Environmental Protection Agency; NYSDEC, New York State 

Department of Environmental Conservation; NYS OPRHP, New York State Office of Parks, Recreation and Historic Preservation; NPS, National Park Service; 

TNC, The Nature Conservancy; FWS, U.S. Fish and Wildlife Service; USACE, U.S. Army Corps of Engineers]

Name Title Organization Email

Darvene Adams Regional Monitoring Coordinator EPA adams.darvene@epa.gov

Sarah Adams-Schoen Assistant Professor of Law and Director of 

the Institute on Land Use and Sustainable 

Development Law

Touro Law School sadams-schoen@tourolaw.edu

Gilbert Anderson Commissioner Suffolk County Brielle.Liere@suffolkcountyny.gov

Ken Arnold Sanitary Engineer Nassau County karnold@nassaucountyny.gov

Seth Ausubel Chief, New York Watershed Management 

Section

EPA Ausubel.Seth@epa.gov

Rick Balla Chief, Watershed Management EPA balla.richard@epa.gov

Bret Bennington Professor of Geology Hofstra University geojbb@hofstra.edu

Vince Biondo Bay Management Specialist Town of Babylon vbiondo@townofbabylon.com

Lorne Birch Planner Town of Hempstead lornbir@TOHmail.org

Henry Bokuniewicz Distinguished Service Professor SoMAS Henry.Bokuniewicz@stonybrook.edu

Betty Borowsky President South Shore Audubon Society bborow@optonline.net

Patti Bourne Director Economic Development City of Long Beach pbourne@longbeachny.gov

Alison Branco Program Director Peconic Estuary Program Alison.Branco@suffolkcountyny.gov

Marshall Brown Director Save the Great South Bay marshall@savethegreatsouthbay.org

Bruce Brownawell Associate Professor SoMAS bruce.brownawell@stonybrook.edu

James Browne Conservation Biologist Town of Hempstead ecojimb@gmail.com

Stuart Buckner Director of Environmental Services Town of Islip sbuckner@townofislip-ny.gov

Marty Byrnes Great Atlantic Shellfish Hatchery Supervisor Great South Bay Hatchery orders@GSBHatchery.com

Tom Carrano Waterways Manager Town of Brookhaven tcarrano@brookhaven.org

Frank Castelli Environmental Projects Coordinator Suffolk County frank.castelli@suffolkcountyny.gov

Beth Christensen Associate Professor Adelphi University Christensen@adelphi.edu

Joe Davenport Chief Sanitary Engineer Unit Head, 

Water/Wastewater Engineering Unit 

Nassau County Department of Public Works

Nassau County jdavenport@nassaucountyny.gov

Walter Dawydiak Division Director of Environmental Quality Suffolk County Walter.Dawydiak@suffolkcountyny.gov

Mary Dempsey Vector Control, Biologist Suffolk County Mary.dempsey@suffolkcountyny.gov

Charles de Quillfeldt Biologist, Bureau of Marine Resources NYSDEC Charles.DeQuillfeldt@dec.ny.gov

Maureen Dolan 

Murphy

Chair, Executive Programs Manager Citizens Campaign for the 

Environment

mmurphy@citizenscampaign.org

Adrienne Esposito Executive Director Citizens Campaign for the 

Environment

aesposito@citizenscampaign.org

Joe Febrizio Deputy Commissioner of Public Works City of Long Beach jfebrizio@longbeachny.gov

Lauretta Fischer Chief Environmental Analyst Suffolk County lauretta.fischer@suffolkcountyny.gov

Charles Flagg Research Professor SoMAS Charles.Flagg@stonybrook.edu

Brian X. Foley Deputy Regional Director for Long Island NYS OPRHP Brian.Foley@parks.ny.gov

Aaren Freeman Associate Professor Adelphi University afreeman@adelphi.edu

Sharon Frost Soil and Water Conservation District TechnicianSuffolk County Sharon.Frost@suffolkcountyny.gov

Dan Fucci Hydrogeologist Department of Public Works Nassau County dfucci@nassaucountyny.gov

Sandra Garren Assistant Professor of Geology, Environment, 

and Sustainability

Hofstra University sandra.j.garren@hofstra.edu

Chris Gobler Associate Professor SoMAS Christopher.Gobler@stonybrook.edu

Anthony Graves Environmental Analyst Town of Brookhaven agraves@brookhaven.org

Jeffrey Greenfield Chair, Nassau County Planning Commission Nassau County jgreenfield@nassaucountyny.gov

Rich Groh Principal Environmental Analyst Town of Babylon rgroh@townofbabylon.com
Appendix 4 95

Table 4–1. Contributors to the meetings at which recommendations were presented for the creation of this document.—Continued

[SoMAS, Stony Brook University School of Marine and Atmospheric Sciences; EPA, U.S. Environmental Protection Agency; NYSDEC, New York State 

Department of Environmental Conservation; NYS OPRHP, New York State Office of Parks, Recreation and Historic Preservation; NPS, National Park Service; 

TNC, The Nature Conservancy; FWS, U.S. Fish and Wildlife Service; USACE, U.S. Army Corps of Engineers]

Name Title Organization Email

Bob Grover Member Great South Bay Audubon 

Society

rgrover@gpinet.com

Joe Guarino Principal Environmental Analyst Town of Babylon jguarino@townofbabylon.com

Daniel J. Gulizio Executive Director Peconic Baykeeper dan@peconicbaykeeper.org

Emerson Hasbrouck Senior Educator Cornell Cooperative Extensionech12@cornell.edu

William Hastback Biologist, Bureau of Marine Resources NYSDEC William.Hastback@dec.ny.gov

Lorraine Holdridge Environmental Engineer II, Division of Water, 

Bureau of Water Resources Management

NYSDEC Lorraine.holdridge@dec.ny.gov

Tom Iwanejko Chief Environmental Analyst Suffolk County Tom.Iwanejko@suffolkcountyny.gov

Kaetlyn Jackson Park Planner NPS kaetlyn_Jackson@nps.gov 

Mike Jensen Associate Public Health Sanitarian Suffolk County michael.jensen@suffolkcountyny.gov

Sheri Lyn Jewhurst Peconic Estuary and New York State Nonpoint 

Source Coordinator

EPA Jewhurst.Sheri@epa.gov

Sean Jordan Deputy Commissioner Town of Oyster Bay sjordan@oysterbay-ny.gov

Carl LoBue Senior Marine Scientist TNC clobue@tnc.org

Chris Lubicich Principal Public Health Engineer Suffolk County chris.lubicich@suffolkcountyny.gov

Trish Manzi Soil and Water Conservation District Manager Nassau County nassauswcd@optonline.net

Tom Marquardt Principal Planner Town of Islip tmarquardt@townofislip-ny.gov

Ryan McTiernan Executive Assistant to the City Manager City of Long Beach rmctiernan@longbeachny.gov

Enrico Nardone Executive Director Seatuck egnardone@seatuck.org

Bob Nyman Regional Coastal Projects Manager EPA nyman.robert@epa.gov

Steve Papa Biologist FWS Steve_Papa@fws.gov

Chris Pickerell Marine Program Director Cornell Cooperative Extensioncp26@cornell.edu

Nancy Pierson Senior Public Health Sanitarian Suffolk County Nancy.Pierson@suffolkcountyny.gov

Jim Ruocco Volunteer Operation SPLASH jim@freeportautoparts.biz

Sean Sallie Senior Planner Nassau County ssallie@nassaucountyny.gov 

Jack Schnirman City Manager City of Long Beach jschnirman@longbeachny.gov

Thomas Schultz Codirector Friends of Bellport Bay BellportBay@optimum.net

Marty Shea Chief Environmental Analyst Town of Southampton mshea@southamptontownny.gov

Robert Smith Biologist, New York District Corps of EngineersUSACE Robert.J.Smith@usace.army.mil

Shavonne Smith Environmental Coordinator Shinnecock Tribe shavonnesmith@shinnecock.org

Chris Soller Superintendent, Fire Island National Seashore NPS chris_soller@nps.gov

Adam Starke Conservation Coordinator TNC astarke@tnc.org

R. Lawrence Swanson Associate Dean, SoMAS, and Director, Waste 

Reduction and Management Institute

SoMAS Larry.Swanson@stonybrook.edu

John Tanacredi Director, Center for Environmental Research 

and Coastal Oceans Monitoring

Molloy College jtanacredi@molloy.edu

Jay Tanski Coastal Processes and Facilities Specialist Cornell Cooperative Extension

jjt3@cornell.edu

Jaime Van Dyke Chair, Nassau County Soil and Water Conservation DistrictTown of Oyster Bay jvandyke@oysterbay-ny.gov

Rob Weltner President Operation SPLASH operationsplash@optonline.net

Tom Wilson Instrument Engineer, Ocean Instrument Laboratory

SoMAS Thomas.Wilson@stonybrook.edu

William Wise Director New York Sea Grant william.wise@stonybrook.edu

Byron Young Member Eastern Long Island Audubon 

Society

youngb53@optimum.net

Appendix 5 97

The first South Shore Estuary Reserve (SSER) Coordinated Water Resources Monitoring Strategy (CWRMS) 

Update Project Advisory Committee (PAC) meeting was held 

at the Town of Babylon Parks and Recreation building and 

included members of the PAC (table 4–1) and other SSER 

stakeholders. The meeting’s objective was to bring together 

Federal, State, Tribal, and local governments; academic institutions; and nonprofit organizations for an informed discussion 

about how the surface water and groundwater within the SSER 

watershed have changed since the first CWRMS was compiled in 2000. Through an agreement between the New York 

State Department of State Office of Planning and Development (NYSDOS) and the U.S. Geological Survey (USGS) 

that commenced in October 2014, the USGS will prepare a 

CWRMS update by 2016 and create a CWRMS website with 

an interactive mapper, which will spatially display water-quality monitoring sites and access water-quality data through the 

Water Quality Portal (https://www.waterqualitydata.us/). Data 

and other pertinent information for this project will primarily 

be solicited from entities and individuals with water-quality 

and (or) ecological expertise in the SSER through a series of 

meetings with the PAC, surveys, a regional workshop, and 

interviews with governmental agencies, academic institutions, 

and nonprofit organizations.

Rich Groh, of the Town of Babylon and a long-standing 

SSER partner, welcomed the group to the PAC meeting. Following a round of introductions, S. Fisher presented slides 

and gave a brief explanation of why the CWRMS is in need 

of a revision, the objectives of the agreement, and the role 

of the PAC. As the presentation progressed, discussion of 

issues related to SSER water quality in the past 15 years was 

facilitated to identify and focus the concerns of the PAC. A 

group discussion followed and identified topics that need to be 

covered in the CWRMS update. These PAC discussion topics 

include

• Groundwater influence to the Reserve bays

• Inadequate onsite wastewater treatment systems 

leading to contaminated groundwater (particularly of 

concern near the coast)

Appendix 5. Notes From the South Shore Estuary Reserve Coordinated Water 

Resources Management Strategy Project Advisory Committee Meetings

• Larger sources of nitrogen and other contaminants 

than previously thought

• Potential sources of pathogens

• Total maximum daily loads (TMDLs)

• Constituents

• Status of existing TMDLs being prepared

• Timelines for completing TMDLs for bays and 

tributaries

• Wastewater

• Point sources such as sewage treatment plant outfalls 

and discharges from illicit wastewater hook-ups

• Nonpoint sources such as overland flow to the bays 

and contributions from groundwater seepage

• Infrastructure concerns—failing/collapsing cesspools, leaking sewage lines, especially from private 

hookups to municipal lines

• Stormwater treatment/retention

• Nassau County Bay Park Sewage Treatment Plant 

and others that discharge to SSER waters

• Suffolk County Southwest Sewer District (Bergen 

Point) and other plants that discharge to the Atlantic 

Ocean

• Sediment

• Physical and chemical data are lacking

• Surface elevation tables (salt marshes)

• Transport

• Water quality of the bays, tributaries, and contributing 

groundwater

South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Update

Project Advisory Committee Meeting #1 Notes

Town of Babylon, Department of Parks and Recreation Building

151 Phelps Lane, North Babylon, NY

Thursday, February 5, 2015 (Snow Date, February 6, 2015)—9:30 a.m.–3:15 p.m.

U.S. Geological Survey—Shawn Fisher and Chris Schubert

New York State Department of State Office of Planning and Development and the South Shore Estuary Reserve Office—

Nancy Rucks, Myra Fedyniak, Sherry Forgash, and Lou Siegel
98 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

• Nutrients

• Pesticides/herbicides

• Petroleum and other organic pollutants

• Pathogens

• Beach and shellfishing closures

• Phytoplankton surveys and harmful algal blooms

• TMDLs

• Personal care products

• Wildlife

• Shellfish monitoring and restoration

• Finfish surveys

• Birds/waterfowl inventory

• Horseshoe crab inventory

• Climate change

• Increased frequency of extreme weather events

• Sea-level rise

• Increased frequency and height of storm surges

• Increased localized spring-tide flooding

• Ocean acidification

• Shoreline resiliency—natural and built

• Salt marshes

• Submerged aquatic vegetation

• Invasive plants

• Vulnerable infrastructure near the shore such as 

home heating, fuel tanks, and septic tanks/cesspools

• Inventory of marinas

• Dredging

• Hurricane Sandy

• Effects on water and sediment quality

• Effects on the built environment

• Rebuilding—dunes, wetlands, homes, marinas, 

wastewater infrastructure, and transportation infrastructure

• Aftermath and looking forward

• Tidal wetland loss

• Spills, contaminants, and floatables databases and 

inventories

• Dredging

• Potential effect of regional projects on water quality, 

including New York Rising Community Reconstruction Plan projects, Rebuild by Design project in Mill 

River (East Rockaway), and Suffolk County sewer 

system upgrades

The group discussed the type and availability of data to 

begin making connections between the topics for the CWRMS 

update and how those data will be referenced and displayed on 

the CRWMS interactive mapper. Each PAC member identified 

one or more sources of data and how/where they are being 

stored. Some of the organizations that have collected and 

stored data pertaining to the SSER were identified as follows:

• U.S. Environmental Protection Agency (EPA)

• U.S. Geological Survey

• U.S. Army Corps of Engineers

• U.S. Fish and Wildlife Service

• National Park Service—Fire Island National Seashore

• National Oceanic and Atmospheric Association

• New York State Department of Environmental Conservation

• New York State Office of Parks, Recreation, and Historic Preservation

• Nassau County

• Suffolk County

• Cornell Cooperative Extension of Suffolk County

• Town of Hempstead

• Town of Babylon

• Town of Southampton

• The Nature Conservancy

• Stony Brook University—School of Marine and Atmospheric Sciences

• Molloy College

• Operation SPLASH

• American Littoral Society

• Adelphi University

• Other citizen science organizations
Appendix 5 99

Using a Microsoft PowerPoint presentation, S. Fisher 

illustrated each SSER CWRMS proposed web page and its 

content. The website will embed the Water Quality Portal 

mapper, which queries the Water Quality Exchange (WQX; 

a search engine of both the EPA Storage and Retrieval 

[STORET] and USGS National Water Information System 

[NWIS] databases). Many topics and data types outlined 

above were suggested for inclusion as layers or data points. 

As the website develops, USGS will work with the PAC to 

design the pages, which will include a PAC member-only 

page (requiring login) that will host all meeting documents, a 

forum, and PAC-related updates.

An SSER CWRMS update workshop has been scheduled 

for May 28, 2015, at Farmingdale State College, Farmingdale, New York, and a draft agenda was shared with the PAC. 

Tentatively, there will be a keynote speaker in the morning 

(Judith Enck, EPA Region 2, was suggested), followed by 

presentations by USGS, NYSDOS, and other stakeholders to 

provide context for the SSER CWRMS update, the current status of SSER water-quality and monitoring activities, and the 

importance of stakeholder input. A series of breakout sessions 

will generate discussion about pertinent topics. The results 

from the workshop will help identify the most important topics 

for the CWRMS update.

The PAC meeting was successful in assembling most 

of the relevant stakeholders who closely monitor the SSER 

to discuss pressing issues facing the SSER bays, tributaries, 

and groundwater. A follow-up meeting for those who were 

unable to attend is being scheduled for March 19, 2015, and 

interviews with water-quality practitioners will be held on an 

individual basis in the coming months. A date for the second 

PAC meeting is to-be-determined—and may be held a few 

weeks before the workshop.

This was the second meeting of the South Shore Estuary 

Reserve (SSER) Coordinated Water Resources Monitoring 

Strategy (CWRMS) Project Advisory Committee (PAC). The 

objective of the meeting was to bring together Federal, State, 

Tribal, and local government agencies, academic institutions, 

and, nonprofit organizations that were unable to attend the first 

PAC meeting on February 5, 2015. Development of the new 

CWRMS and monitoring information repository (website/

mapper) commenced in October 2014 through an agreement 

between the New York State Department of State (NYSDOS) 

Office of Planning and Development and the U.S. Geological 

Survey (USGS).

Using a Microsoft PowerPoint presentation, S. Fisher 

explained the new CWRMS project, the agreement tasks, and 

the role of the PAC. As the presentation progressed, discussion of issues related to SSER water quality in the past 15 

years was facilitated to identify and focus the concerns of the 

PAC members. This was followed by a discussion of topics 

for the new CWRMS. The following is a summary of the PAC 

member discussions:

• Purpose of the CWRMS strategy and website is to create a cohesive, prioritized, user-friendly clearinghouse 

for environmental data for the SSER and its groundwater contributing area and not just a list of available 

information

• The NYSDOS is still planning on updating the SSER 

Comprehensive Management Plan (CMP) in the future

• The SSER Office is currently preparing the SSER CMP 

Implementation Status Report

• The SSER CMP update will look at potential amendments to the Long Island SSER Act

• Data archiving emerged as a followup project to the 

CWRMS. Data transferred into the Water Quality 

Exchange (WQX), which is a search engine that queries both the U.S. Environmental Protection Agency 

(EPA) Storage and Retrieval (STORET) and USGS 

National Water Information System (NWIS) databases, 

will be permanently archived and available for use 

thereby safeguarding legacy datasets; the type of data, 

units, and mode of storage need to be addressed

• Data sharing agreements between agencies or academics may be needed

South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Update

Project Advisory Committee Meeting #1–A Notes

State Office Building, Basement Classroom

250 Veterans Memorial Highway, Hauppauge, NY

Thursday, March 19, 2015—9:00 a.m.–12:00 p.m.

U.S. Geological Survey—Shawn Fisher and Chris Schubert

New York State Department of State Office of Planning and Development Office—Nancy Rucks and Myra Fedyniak;

Long Island South Shore Estuary Reserve Office—Sherry Forgash and Lou Siegel

PAC Members

The meeting began at 9:15 a.m.
100 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

• The PAC should prioritize how and when information 

for the CWRMS and the website will be updated

• There are some problems with the WQX in terms of 

data units—it was suggested that a PAC meeting be 

held specifically to learn how to work with the WQX

• Types of data that should be entered into the WQX

• Stormwater/wastewater/groundwater data

• Sediment sampling/contamination data

• Sea-level rise data and effect on marshes

• Invasive species data

• Shellfish health data

• Biota inventories

• The CWRMS should have an ecosystem-based management (EBM) focus

• Portions of the Peconic Estuary Program submerged 

aquatic vegetation management plan that are applicable 

to the SSER should be included

Available data that should be presented in the CWRMS and 

(or) the website interactive mapper:

• Utilize the Long Island Geographic Information Systems User Group, data.gov, and Sea Grant (searchable 

database for legacy studies) for data and information

• Open space and land-use datasets (for lands surrounding the SSER and its tributaries)

• Recreational and commercial loadings (fishing) data

• Monitoring data on marsh restoration projects

• Data on capital improvement projects (such as those 

funded by the New York Rising Community Reconstruction Program and U.S. Army Corps of Engineers 

[USACE])

• Bird data (such as nesting Saltmarsh Sparrow data 

from the U.S. Fish and Wildlife Service [FWS])

• Data from horseshoe crab research and other wildlife 

monitoring programs

• Tidal wetlands trends analysis data

• Surface elevation tables (for measuring relative sediment elevation changes for tidal marsh monitoring)

• Harmful algal bloom data

• Marine debris data

• Data from sewage treatment plants and public drinking 

water wells

• Water-quality monitoring data (such as data collected 

by Stony Brook University School of Marine and 

Atmospheric Sciences [SoMAS]) in Great South Bay 

that dates back to 2004 and includes temperature, 

salinity, chlorophyll, and water level. Real-time data 

are provided by seven monitoring sites from Tanner 

Park in Babylon to Smith Point in Brookhaven, a buoy 

south of Sayville, and the Sea-Bird SeaCat off Bellport. SoMAS also collects data from periodic aerial 

flights, photomosaics, bathymetric surveys, and nutrient sampling at the Old Inlet breach. There are also 

USGS real-time water-quality monitoring stations in 

Hog Island Channel and Reynolds Channel.

• Data from additional nongovernment groups that do 

citizen monitoring including Trout Unlimited; Operation SPLASH; Coastal Research and Education Society 

of Long Island (CRESLI), which has a good amount 

of data, and other organizations collecting data on alewives, seafood, marine debris, and birds. The Seafood 

Council is another source of information

• Water-quality data from public beaches and closures 

(State and local)

• Data regarding runoff from stormwater inputs, golf 

courses, and municipal separate storm sewer system 

(MS4) information from government agencies

• National Coastal Condition Assessment data (which 

is completed every 5 years and includes sediment 

chemistry, fish studies, and discharge monitoring—the 

Bay Park Sewage Treatment Plant will be included in 

monitoring efforts this year)

• Studies being completed on the western bays by 

Queens College

• Sea-level rise (SLR) modeling by CDM-Smith, consultants

• Applicable aquaculture data from the Peconic Estuary 

Program

• Study of the Grand Canal in Oakdale

• USACE Northeast Coast Comprehensive Study (Nassau County is a potential study site)

• Source Water Assessment Program

• USGS monitoring data (which includes groundwater 

contributing areas, major streams monitoring, and continuous water-quality monitoring gages (temperature, 

salinity, total chlorophyll, turbidity, dissolved oxygen, 

and nitrate). Plans include installing tide gages on barrier side of Great South Bay (Moriches, Shinnecock, 

and West Sayville). Post-Hurricane Sandy, USGS 

collected 120,160 samples for metals, polychlorinated 

biphenyls (PCBs), and dioxin along the New York and 
Appendix 5 101

New Jersey coast and will be starting a new sampling 

project to collect baseline sediment data from Maine to 

Virginia.

S. Fisher showed slides of the proposed SSER CWRMS 

website. The website will embed the Water Quality Portal 

mapper, which queries both NWIS and STORET. Many topics 

and data types outlined above were suggested for inclusion 

as layers or as data points. As the website develops, USGS 

will work with PAC members to design the pages, which will 

include a PAC member-only page (requiring login) that will 

host meeting documents and reports for review, a forum, and 

PAC-related updates. Adding a key word search to the references section of the website was suggested.

An all-day SSER CWRMS workshop is scheduled for 

May 28, 2015, at Farmingdale State College, Farmingdale, 

N.Y. The draft agenda includes a morning keynote speaker, 

followed by presentations by USGS, NYSDOS, and other 

stakeholders to provide context for the new SSER CWRMS, 

the status of SSER water-quality and monitoring activities, 

and the importance of stakeholder input. A series of breakout 

sessions in the afternoon will generate discussion about topics 

pertinent to the SSER. The results from the workshop will 

help identify available datasets and the most important topics 

for the new CWRMS. Discussion of the workshop included:

• Topic suggestions for breakout sessions

• Hurricane Sandy (and coastal storms in general)

• Harmful algal blooms, acidification

• Fire Island to Montauk Point (FIMP) Reformulation 

Study

• Comparing the eastern and western SSER bays

• Poster presentations covering additional topics not 

discussed by the panelists

USGS will be in contact with PAC members to schedule 

individual meetings after the CWRMS workshop to gather 

information that is more specific.

Meeting adjourned at 12:15 p.m.

This was the second all-hands meeting of the South 

Shore Estuary Reserve (SSER) Coordinated Water Resources 

Monitoring Strategy (CWRMS) Project Advisory Committee 

(PAC). The objective of the meeting was to update the PAC on 

the current status of the CWRMS and demonstrate the website 

forum feature.

Sarah Adams-Schoen of Touro welcomed the PAC to 

campus and provided information on logistics for the meeting.

Using a Microsoft PowerPoint presentation, S. Fisher 

reviewed the highlights of the previous PAC meetings and the 

CWRMS workshop held at Farmingdale State College on May 

29, 2015. The individual stakeholder meetings were mentioned 

as most have been completed and notes, which will be used to 

help draft the CWRMS document, have been drafted. There 

was a brief discussion about how these notes would be used in 

shaping the document.

Following a discussion of milestones reached thus far, 

a draft outline for the CWRMS document was presented and 

the PAC was asked to comment. Each item was reviewed and 

discussed, with changes made in real time. There were many 

good suggestions for making the structure of the report better. 

See the attached revised version of the draft CWRMS outline.

A draft of the “Quality Assurance and Quality Control” (QA/QC) section of the CWRMS report was presented 

next. Changes were again made in real time, with discussion 

focused on the level of QA/QC groups (agencies, academics, citizen scientists) are responsible for, how much can be 

expected of them, and whether they should be following a 

quality assurance project plan (QAPP) or QAPP-like document regardless of how funding is provided. See the attached 

revised version of the draft QA/QC section outline.

L. Bonavita gave an interactive demonstration of the 

CWRMS website and forum. Each page on the public-facing 

portion of the website was reviewed. The PAC member forum 

was then introduced as a login-based system for the exchange 

of documents and conversation related to monitoring in the 

SSER. As most PAC members had an internet-enabled device, 

they were able to register and follow along inreal time. Functions such as messaging, creating forum threads, and uploading documents were reviewed, and an instructional pamphlet 

was provided for future reference. There were several questions and requests for additional functions and fixing bugs.

After the CWRMS website demonstration, S. Fisher 

reviewed how the Water Quality Exchange (WQX) is set 

South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy Update

Project Advisory Committee Meeting #2 Notes

Touro Law School, Central Islip, NY

Friday, September 18, 2015—9:00 a.m.–3:00 p.m.

U.S. Geological Survey—Shawn Fisher and Chris Schubert

New York State Department of State Office of Planning and Development Office—Nancy Rucks

Long Island South Shore Estuary Reserve Office—Sherry Forgash

Project Advisory Committee Members—See attached sign-in sheet for attendees.

The meeting began at 9:15 a.m.
102 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

up and how data can be uploaded. Although the ability to 

conduct a full demonstration of the WQX was not available, examples of the data types and the U.S. Environmental 

Protection Agency (EPA) Central Data Exchange website 

were shown and explained. Only a few PAC members felt that 

their agency’s data could be fit into the WQX templates and 

uploaded for public use. The type of data, units, and mode of 

storage was mentioned again and needs to be addressed on an 

individual user basis.

Other topics of discussion throughout the day included:

• The Office of Planning and Development (OPD) is 

still planning on updating the SSER Comprehensive 

Management Plan (CMP) in the future

• The OPD plans to follow up on the action items set 

forth in the CWRMS with funding opportunities

• The OPD will look to continue collaboration with 

USGS and other partners/stakeholders studying the 

SSER

• There are data repositories other than EPA STORET 

that are more amenable to taking in continuous waterquality monitoring data

A brief review of “next steps” for creating the CWRMS 

and updating the project website was given at the end of the 

meeting.

USGS will be in contact with PAC members to provide 

updates on the CWRMS website and as the report is being 

drafted.

Meeting adjourned at 3:00 p.m.

U.S. Geological Survey

Project Advisory Committee (PAC) Meeting 3 for the Long Island South Shore Estuary Reserve (SSER)

Coordinated Water Resources Monitoring Strategy (CWRMS) project

The Suffolk Center

Molloy College

7180 Republic Airport, East Farmingdale, NY 11735

Thursday, October 27, 2016

8:30 a.m.–12:30 p.m.

Attending:

Staff:

Shawn Fisher, U.S. Geological Survey (USGS)

Jason Finkelstein, USGS

Rob Welk, USGS

Jeremy Campbell, New York State Department of State (NYSDOS) Office of Planning and Development (OPD)

Sherry Forgash, NYSDOS OPD SSER Office

Lou Siegel, NYSDOS OPD SSER Office

PAC Members:

James Browne, Town of Hempstead

Marty Byrnes, Town of Islip

Charles de Quillfeldt, New York State Department of Environmental Conservation (NYSDEC)

Maureen Dolan Murphy, Citizens Campaign for the Environment

Dan Fucci, Nassau County Department of Public Works

Rich Groh, Town of Babylon

Mike Jensen, Suffolk County Department of Health Services

Tom Marquardt, Town of Islip

Bob Nyman, U.S. Environmental Protection Agency (EPA)

Adam Starke, The Nature Conservancy

John Tanacredi, Molloy College

Phil DeGaetano, New England Interstate Water Pollution Control Commission

Ruth Coffey, Adelphi University

Evelyn Powers, Interstate Environmental Commission
Appendix 5 103

S. Fisher began the third Project Advisory Committee 

(PAC) meeting for the Coordinated Water Resources Monitoring Strategy (CWRMS) NYSDOS funded project at 9:19 a.m. 

The project was summarized and updates provided, including items covered at previous PAC meetings, a description of 

groundwater contributions to the bays, and a short explanation of the progress of the website and mapper. The agenda 

for the day’s meeting was provided and included overview of 

the mapper and its current layers, discussion of review of the 

report chapters, including data gaps and recommendations, 

and outline of the final steps before publication.

The first draft of the CWRMS has been sent to approximately 90 PAC members. The plan is to provide the existing 

project website to NYSDOS to continue and maintain. Should 

the NYSDEC and NYSDOS decide to expand the mapper to 

the rest of Long Island as part of the NYSDEC Long Island 

Nitrogen Action Plan (LINAP), the USGS would leverage the 

existing work and maintain control of the site for an additional 

length of time.

S. Fisher mentioned the Water Quality Exchange/Portal 

as a way of archiving and preserving current and historical 

water-quality and certain ecological data.

R. Welk led the interactive portion of the meeting with 

a demonstration on the features of the project website and 

mapper. Both the website and mapper are functional, but a 

newer version of the mapper is in the works and planned for 

release in the coming months. He explained that the future 

mapper will have filtering capabilities and be more effective 

at supporting management decisions and identifying data 

gaps as well as potential collaborative partnerships. Data will 

be searchable based on hydrologic unit codes, monitoring 

agency, constituents collected, and collection frequency. On 

the current map, different colors of dots on the mapper refer 

to the frequency of sampling while the shape of the point refer 

to type of site (for example, estuary, groundwater, stream) at 

which data are available. R. Welk provided more details about 

the information contained in the drop-down box that appears 

after clicking on one of the dots on the mapper. The data are 

generally presented in the mapper in the manner it is provided 

to USGS, but is subject to modification, if necessary. All datasets will be accessible; trying not to duplicate efforts.

J. Tanacredi noted that infrastructure should be included 

on the mapper, such as location of outfalls. S. Fisher replied 

that USGS has been actively pursuing these datasets from the 

towns and counties but has not yet obtained it. He also asked if 

U.S. Army Corps of Engineers (USACE) permits for dredging be identified on the mapper? R. Welk said the USACE has 

static PDFs available online with permit information, but no 

shapefiles are available. L. Siegel explained that a NYSDOS 

funded project, “Planning for Dredged Materials Management,” may have shapefiles associated with it; these should 

be included on the CWRMS website. J. Browne said Town 

of Hempstead’s historic dredging and borrow pit data are not 

available. R. Groh suggested including total maximum daily 

load (TMDL) waterbodies and uncertified shellfish waters on 

the website. S. Fisher noted that the shellfish areas could be 

included in the website, but that the information would only 

point to where open or closed shellfish areas could be found. 

The TMDL listing will indicate health of the bays concerning constituents, such as nitrogen and pathogens. USGS has 

the Priority Waterbodies List link on the website, which notes 

additional impairments.

J. Campbell asked if there is a mechanism or process 

for updating the data on the project website, specifically the 

mapper. J. Finkelstein noted that new datasets are added easily; obtaining the data from stakeholders can be difficult. R. 

Nyman said there should be a method for dating the database. 

Updates could pose a problem when the project ends, as it is 

unclear which parties will provide updates to the project website. It was suggested that perhaps USGS can update the data 

annually. S. Fisher said that USGS is trying to automate some 

data to dynamically link it to, as an example, EPA Storage 

and Retrieval (STORET). R. Nyman asked if there was a way 

that users could view the date of the most recent data accessed 

through the project mapper. J. Campbell notes that there is 

interest from NYSDEC and the LINAP project to expand the 

mapper for island-wide coverage. USGS will attempt to automate the website as much as possible.

L. Siegel described how there needs to be a mechanism 

(a system) to report to NYSDOS SSER Office and USGS, 

who is collecting data, what type of data are being monitored, 

when the data are being collected, and location of monitoring. All stakeholders should be reporting their work. It was 

suggested that a form (perhaps a web-based reporting system) 

should be sent to stakeholders to complete and submit to the 

SSER Office to help inform recommendations to monitoring 

programs and encourage coordination. R. Welk mentioned that 

the website forum is not being used as much as it could. R. 

Nyman commented on the need for a strategy for collection 

and use of data.

C. de Quillfeldt said that the next version of the SSER 

Comprehensive Management Plan (CMP) should include the 

projects that still need to be implemented. He also feels that 

the current draft of the CWRMS is lacking in some areas; 

it needs a better focus for sampling and it is missing some 

recommendations.

J. Tanacredi suggested that the CWRMS include land use 

issues/patterns, especially in the watersheds of Great South 

Bay. He cited the vast number (approximately 3,500) of new 

housing units and the potential for water-quality impacts.

R. Groh asked if a polygon layer for sewered versus 

unsewered areas would be added. C. DeQuillfeldt noted 

that most of the south shore of Suffolk County is not being 

sewered and that inland treatment plants discharge effluent to 

groundwater.

E. Powers asked if the mapper will have the capacity and 

the functionality to accommodate more layers. J. Finkelstein 

responded that more layers can be added if the data were 

provided.
104 Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

CWRMS Chapter 1: Introduction1

S. Fisher solicited comments from the PAC and informed 

them that comments can still be submitted.

J. Tanacredi wants to see an established ecological assessment of the bays with baseline data, such as inventories and 

indices, included in cdm chapter 1. L. Siegel reminded all that 

the 2001 SSER CMP includes numerous technical reports that 

were written to inform the CMP that provide baseline inventories. Additionally, The Nature Conservancy wrote a comprehensive report on the Great South Bay. The final watershed 

management plans contain the status of various areas within 

that particular watershed.

There was mention of the former duck farms and their 

legacy contribution to nitrogen impairments.

S. Fisher asked the PAC their opinion on including 

trophic state indicators (TSIs) and forcing functions in chapter 

1. In the draft, these are both included in chapter 1, but they 

could possibly be separated and more information could be 

provided. No opposition to the draft’s structure was expressed 

regarding this issue.

CWRMS Chapter 2: Resource Monitoring in the Long 

Island South Shore Estuary Reserve

C. de Quillfeldt suggested including the glass eel survey 

conducted by NYSDEC in Carmans River (and possibly 

Massapequa Creek).

S. Fisher described the report Table 6of instrumentation 

used for data collection by PAC members. The idea is to get a 

sense for what technology is available and whether is effective 

for measuring physical constituents. For chemical constituents, 

laboratory procedures are to be documented.

T. Marquardt noted the importance of monitoring waterquality post-aquaculture as being analogous to best management practices or green infrastructure (BMP). Environmental 

assessments and in situ nitrogen-removal studies should be 

conducted to understand the effectiveness of shellfisheries and 

other BMPs.

M. Dolan-Murphy suggested that a paragraph on ocean 

acidification is needed in the report—this is an urgent issue 

that could be addressed with a task force. pH data are a major 

gap. A gap also exists regarding microplastics in the SSER 

(loads, in the sediment, in marine life, etc.).

The NYSDEC provides for monitoring air resources. 

Nassau and Suffolk Counties have had increased ozone levels. 

Data on contribution of atmospheric nitrogen to the estuary is 

needed.

Partial pressure of carbon dioxide is a data gap. This is 

not easy to measure. J. Browne noted that Town of Hempstead 

has the capacity to measure it but needs funding.

1

Chapter numbers are not included in the finalized CWRMS.

CWRMS Chapter 3: Quality Assurance and Quality 

Control, Metadata, and Data Archives

Other groups who do monitoring through their own 

grants should be encouraged to move that data to a national 

registry.

J. Campbell noted that the NYSDEC will not use data 

from citizen science groups without a quality assurance project 

plan (QAPP).

The EPA can assist groups in writing a QAPP.

S. Fisher described a ranking system that the State of 

Indiana uses to indicate the degree of quality assurance and 

quality control (QA/QC) associated with monitoring program. 

Data can be described as tier 1, tier 2, or tier 3, with ascending numbers indicating a higher level of data. For example, 

only tier 3 is used by the NYSDEC for regulatory purposes. 

At this point, a discussion on QA/QC developed. J. Tanacredi expressed concern that monitoring programs without a 

QAPP (and tier 3) status were not useful. A. Starke and others 

insisted that all data are important, and that tier 1 and tier 2 

are necessary as ways of identifying waterbodies of concern. 

J. Campbell suggested contacting the NYSDEC to discuss the 

process of citizen science and academia developing QAPPs. 

The QAPPs provide consistency in sampling data for the Protected Waterbodies List.

S. Fisher expressed the necessity of collecting and 

preserving metadata. A good example is the National Park 

Service (NPS) Integrated Resource Management Applications 

(IRMA), which keeps all programs organized so information 

can be made available. This method for documenting and 

archiving studies, data, and metadata conducted within NPS 

boundaries would be a good model for future SSER Office 

record keeping (as mentioned earlier in the meeting)

CWRMS Chapter 6: Coordinated Water Resources 

Monitoring Strategy Website

S. Fisher noted that most of this was discussed earlier in 

the meeting, and there were no additional comments.

CWRMS Chapter 4: Data Gaps and Specific 

Recommendations

S. Fisher asked the PAC to review and complete the 

data gap questionnaire, which will rank each listed gap as 

high, medium, or low priority based on their organizations’ 

missions.

Some PAC members asked if any monitoring was done 

on land, for example, the mapping of, or monitoring at, 

stormwater outfalls. The towns had to complete the mapping 

of stormwater outfalls as part of the municipal separate storm 

sewer system (MS4) program. Stormwater outfall information 

is available. S. Fisher noted that a suggestion was made during 

the individual meetings to use citizen science and Global Positioning System (GPS) to locate all storm drains and to store 

this data in one central location.
Appendix 5 105

J. Tanacredi reiterated the need for a complete inventory 

of the ecosystem health of Great South Bay.

S. Fisher explained that USGS aim in this chapter is to 

capture all the recommendations of the PAC and include them 

in the report tables. L. Siegel suggested converting the tables 

to Microsoft Access; but S. Fisher said this cannot be done, as 

USGS is required to present their information in a basic format 

that is accessible by all, and not everyone who will need this 

data has the Access program (and even the Microsoft Excel 

files currently used will be converted to CSV). That said, an 

Access database can be created and maintained by the SSER 

Office for continued use.

CWRMS Chapter 5: General and Coordination 

Recommendations From the Project Advisory Committee

J. Tanacredi stated that he has made comments, and in 

particular on page 55 of the draft CWRMS; these comments 

will be presented to the USGS for incorporation.

J. Campbell reminded the PAC that there is a link to all 

the Governor’s Office of Storm Recovery (GOSR) NY Rising 

Community Reconstruction plans on the NYSDOS website: http://www.stormrecovery.ny.gov/community-regions/

long-island.

A. Starke asked if economic information would be 

included, such as catch rates. J. Campbell expressed that this 

would be part of the CMP instead.

The PAC meeting concluded at 12:13 p.m.

For more information about this report, contact:

Director, New York Water Science Center

U.S. Geological Survey

2045 Route 112, Building 4

Coram, NY 11727

dc_ny@usgs.gov

(518) 285–5602

or visit our website at

https://ny.water.usgs.gov

Publishing support provided by the 

Pembroke Publishing Service Center
Fisher and others—Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy—Open-File Report 2017–1161

ISSN 2331-1258 (online)

https://doi.org/10.3133/ofr20171161