2009

NEW YORK HARBOR

WATER QUALITY REPORT

Michael R. Bloomberg, Mayor

Caswell F. Holloway, Commissioner
Cover photo: A flock of Double-crested Cormorants, American Oystercatchers and Common Terns in Jamaica Bay
1

2009

NEW YORK HARBOR

WATER QUALITY REPORT
2009 New York Harbor Water Quality Report

2

August 2010

Dear Friends:

This report marks a significant milestone for New York City: the 100th year of comprehensive water quality monitoring of

New York Harbor.

As a result of intensive investments, our harbor waters are healthier today than they have been in a century. Our Administration

has made water quality improvements a top priority, and aquatic life is now thriving in many areas. As part of PlaNYC, our

comprehensive plan for building a truly sustainable city, we are committed to opening 90 percent of our waterways for

recreational use by 2030.

The full account presented here of the health of New York Harbor shows the significant improvements we’ve made — and is

another important step in our efforts to build a greener, greater New York in the years to come.

Sincerely,

Michael R. Bloomberg

Mayor

The New York City Department of Environmental Protection (DEP) is proud to present the 2009 Harbor Water Quality Report,

which reviews the health of New York City’s waterways. DEP treats more than a billion gallons of wastewater that New Yorkers

produce every day, and Mayor Bloomberg has invested billions of dollars to enhance that treatment — and thereby improve

water quality throughout New York Harbor. We are also making unprecedented investments to increase stormwater capture,

which reduces the combined sewer overflows (CSOs) into our surrounding waterways. Based on actual rainfall data, our combined

CSO capture rate was 76 percent in 2009, and we expect that amount to increase as new investments like the Paerdegat Basin

and Alley Creek CSO Retention Facilities go online. The CSO Long-Term Control Plan, the Bronx River Floatables Control

program, and the removal of CSO sediments at outfalls across the City will also increase protection of the City’s waterways.

In 2010 our success has continued. In February, we announced that New York City’s 14 wastewater treatment plants are

meeting monthly Clean Water Act standards for pollutant removal — for the first time ever. And just last month we started

removing 4000 pounds per day of nitrogen from our discharges to Jamaica Bay — the first milestone in a historic agreement

that Mayor Bloomberg announced this past spring.

The City is adopting sustainable, low impact strategies as it incorporates green infrastructure as a central element of its current

and future efforts to reduce CSOs. Green infrastructure adds trees, vegetation and other natural features to our local streetscapes

and prevents pollution from occurring by capturing rainwater before it enters our sewer system. These projects are costeffective and beautify our communities, too! Reorienting our approach to capturing stormwater and preventing CSOs will

require a great deal of coordination with community, business, agency, state, and federal partners, and we look forward to

working with them as we move forward with innovative and sustainable solutions.

Sincerely,

Caswell F. Holloway

Commissioner

T HE C ITY OF N EW Y ORK

O FFICE OF THE M AYOR

N EW Y ORK , N Y 10007

 

 

 

 

 

 
2009 New York Harbor Water Quality Report

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Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4

Synopsis of Four Major Indicators of Environmental Change . . . . . . . . . . . . . . . . . . . . . . .5

Inner Harbor Area

Fecal Coliform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6

Dissolved Oxygen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Chlorophyll ‘a’ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8

Secchi Transparency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Upper East River – Western Long Island Sound

Fecal Coliform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10

Dissolved Oxygen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

Chlorophyll ‘a’ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12

Secchi Transparency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13

Jamaica Bay

Fecal Coliform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14

Dissolved Oxygen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Chlorophyll ‘a’ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16

Secchi Transparency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17

Lower New York Bay – Raritan Bay

Fecal Coliform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18

Dissolved Oxygen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19

Chlorophyll ‘a’ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20

Secchi Transparency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21

Harbor-Wide Improvements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22

Harbor-Wide Water Quality Improvements

Fecal Coliform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

Dissolved Oxygen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24

Chlorophyll ‘a’ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

2009 NYC DEP Harbor Survey Stations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26

NYC DEP Wastewater Treatment Plants and CSOs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28

Table of Contents
2009 New York Harbor Water Quality Report

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he City of New York’s (City) Harbor Survey Program

is one of the longest continuous regional water

quality monitoring programs in the United States,

reaching its 100th year in 2009. The milestones achieved

since the program started a century ago are being

documented in a separate report that will be published

this fall to celebrate the program’s centennial.

The Harbor Survey has greatly evolved from the initial

monitoring efforts conducted by the Metropolitan

Sewerage Commission during 1909, which were done

in response to public outcry about fouled waterways

impacting their quality of life. At the time a handful of

locations around Manhattan were assessed. The survey

grew over the years to encompass the entire City, now

consisting of 55 stations: 36 stations located throughout

the open waters of the harbor, and 19 stations located

in smaller tributaries. The number of water quality

parameters measured has also increased from five in

1909 to more than 20 today.

Throughout the past century, harbor water quality has

improved dramatically. Within the last generation, many

New Yorkers have again begun to use local waterways

for recreation. These improvements in water quality

have been directly associated with infrastructure

investments, including major construction and upgrades

at all 14 in-City wastewater treatment plants (WWTPs)

and increased capture of storm runoff. Today, all sewage

generated in the City on a dry-weather day is now

treated to full Clean Water Act standards.

To further improve and protect New York City’s ambient

waterways, DEP has been investing in sustainable

practices to address flooding, conducting programs to

remove floatables and debris from the waterways, and

organizing beach clean-ups and protection programs.

These include the Floatable Action and Boom and Skim

program, Shoreline Survey–Sentinel Monitoring, and

Enhanced Beach Protection programs. Wet Weather

capture is being addressed by the construction of

combined sewage overflow (CSO) retention tanks and

the introduction of Best Management Practices (BMPs),

also known as green infrastructure, to capture run-off

and reduce flooding in parts of the city. DEP’s Long Term

Control Plan (LTCP) is evaluating still-impaired water

bodies and their drainage basins in the city. Its goal is

to develop comprehensive plans that will attain and

maintain each waterbody’s “best use” classification,

based on NYS Department of Environmental

Conservation (DEC) standards.

This Annual New York Harbor Water Quality Report

includes data collected by DEP during 2009. It is

presented in four sections, each delineating a geographic

region within the harbor. Four water quality parameters,

used as key indicators, are evaluated: fecal coliform

bacteria, dissolved oxygen, chlorophyll ‘a’ and Secchi

transparency. A discussion of enterococci bacteria,

which US EPA is now using as a sewage indicator, is

also included in this year’s report.

Introduction

T

The breeze and the views are perfect for sailing in Jamaica Bay
2009 New York Harbor Water Quality Report

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Fecal Coliform (FC) Bacteria – Fecal coliform

concentrations are measured in NY Harbor as human

health-related indicators of sewage-related pollution.

Fecal coliform are a group of bacteria primarily found in

human and animal intestines and are associated with

sewage waste. These bacteria are widely used as

indicator organisms to show the presence of such

wastes in water and the possible presence of pathogenic

(disease-producing) bacteria.

Chlorophyll ‘a’ – Chlorophyll ‘a’ is a green pigment

found in most macro-algae and phytoplankton. It is

vital for photosynthesis, which allows plants to obtain

energy from light. Chlorophyll ‘a’ found in phytoplankton

can be used as an indicator of primary productivity,

which is the necessary base of the food chain in the

water. These organisms respond quickly to environmental

changes, and their abundance may serve as a measure of

water and ecosystem quality. Overgrowth of primary

producers can cause eutrophication. Chlorophyll ‘a’

levels above 20 ug/L are considered indicative of

enriched, eutrophic conditions.

Eutrophication – Eutrophication is an increase in the

rate of organic matter in an ecosystem, a common

phenomenon in marine coastal waters. In contrast to

freshwater systems, nitrogen is more commonly the key

limiting nutrient of marine waters; thus, nitrogen levels

have greater importance to understanding eutrophication

problems in salt water.

Dissolved Oxygen (DO) – The levels of oxygen

dissolved in the water column are critical for respiration

of most aquatic life forms, including fish and invertebrates such as crabs, clams, zooplankton, etc. Dissolved

oxygen concentration is, therefore, one of the most

universal indicators of overall water quality and a means

of determining habitat and ecosystem conditions.

Secchi Transparency – A Secchi disk is used to estimate

the clarity of surface waters. High Secchi transparency

(greater than 5.0 feet) is indicative of clear water, with

declines in transparency typically due to high suspended

solids concentrations or plankton blooms. Low Secchi

readings (less than 3.0 feet) are typically associated with

degraded waters. These conditions are indicative of light

limiting conditions, which in turn affect primary

productivity and nutrient cycling.

Synopsis of Four Major Indicators

of Environmental Change

Coliform and dissolved oxygen indicators are used in New York State Department of Environmental Conservation

(NYSDEC) standards to quantify ecosystem health or degradation. NYSDEC standards reflect a range of acceptable

water quality conditions corresponding to the State-designated “best usage” of the water body. Common uses and

NYSDEC standards for fecal coliform and dissolved oxygen are noted in the following chart.

Common Water Use and NYSDEC Standards

For Fresh and Saline Waters

Dissolved Oxygen

Class Best Usage of Waters Fecal Coliform (never-less-than) Enterococcus

SA Shellfishing and all No standard 5.0 mg/L

other recreational use

(Monthly geometric mean)

<35 Cells / 100ml SB Bathing and other Monthly geometric mean less than or equal to 5.0 mg/L

recreational use 200 cells/100mL from 5 or more samples (single sample)

Max 104 Cells / 100ml

I Fishing or boating Monthly geometric mean less than or equal to 4.0 mg/L

2,000 cells/100mL from 5 or more samples

SD Fish survival No standard 3.0 mg/L
2009 New York Harbor Water Quality Report

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Water quality as estimated by fecal coliform (FC)

concentrations was superior for the Inner Harbor

in the summer of 2009. The regional average was

39 cells/100 mL, increasing from 19 cells/100 mL in

2008. All monitoring sites in the area complied with

the monthly FC standard of 200 cells/100 mL.

Past data has indicated that the Inner Harbor is prone

to episodic degradation following rain events due to

additional FC loadings from storm drains and combined

sewer overflows (CSOs). Under these conditions, 12 of 13

Inner Harbor Area

FECAL COLIFORM

The Inner Harbor is defined as the area

including: the Hudson River from the

NYC-Westchester line, through the

Battery to the Verrazano Narrows; the

Lower East River to the Battery; and

the Kill Van Kull-Arthur Kill system.

This area contains 13 Harbor Survey

monitoring stations that have been

grouped together due to common

water uses and functions as well as

similarities in point-source loadings.

Waters of the Inner Harbor are often

continuous, through connecting

branches or straits, and cover a large

and diverse geographic expanse.

Most of the Inner Harbor Area,

excluding the Kills, is classified by

NYSDEC as I, for uses such as fishing

or boating. Most of the area in the Kills

is classified for fish survival only (SD),

with the exception of the far southern

reach of Arthur Kill, which is designated

as Class I. The Hudson River, from

North of Spuyten Duyvil to Westchester

County, is designated for Bathing (SB).

sites exceeded the Bathing Standard. Note: Wet Weather

advisories for the New York City beaches may still be

issued by NYC DOHMH under certain conditions.

Water quality as estimated by Enterococcus

concentrations was also superior for the Inner Harbor

in 2009. The regional summer geometric mean was

6 cells/100 mL; all monitoring sites had averages

<10 cells/100 mL which complied with the Bathing

Standard of 35 cells/100 mL for Enterococcus.
2009 New York Harbor Water Quality Report

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DISSOLVED OXYGEN

T R E N D S

Fecal coliform levels in the Inner Harbor have dramatically

declined over the last three decades, with levels since

1997 well below the Bathing Standard. The averaged FC

counts have declined from 2000 cells/100 mL in the

early ’70s to below 100 cells/100 mL since early 1990.

This improvement has allowed for the opening of Inner

Harbor waters to most recreational activities. The

progress has been attributed to the cessation of raw

sewage dumping through the full build-out of New York

City’s Wastewater Treatment Plants (WTPs), the

elimination of illegal discharges into the waterbody and

the reduction of CSOs. Year-to-year variations have

become more apparent with the reduction of FC to

levels below standards.

In 2009, summer Dissolved Oxygen (DO) values averaged

6.5 mg/L for surface waters and 5.8 mg/L for bottom

waters. They were down from 2008 values of 7.4 mg/L

for surface waters and 6.6 mg/L for bottom waters.

Discrete DO measurements of surface and bottom

waters complied with NYSDEC standards 97% and 92%

of the time for surface and bottom waters. There was a

total of 17 to 18 samples taken for each sampling location

during the summer (June–September) 2009.

T R E N D S

Average summer surface DO values in the Inner Harbor

have risen to levels above NYSDEC standards for

primary contact recreation and commercial fisheries

since the late 1980s. Bottom water DO values have

risen from approximately 3.0 mg/L in 1970 to 5.8 mg/L

at present. There is an increase between 0.4–1.3 mg/L for

each decade.

Enterococcus levels in the Inner Harbor have been

monitored since 2001. The averages for the past nine

years have been consistently well below the Bathing

Standard of 35 cells/100 mL.

Herring Gull enjoying a snack
2009 New York Harbor Water Quality Report

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Inner Harbor Area

CHLOROPHYLL ‘a’

The average chlorophyll ‘a’ concentration in the Inner

Harbor was 6.0 ug/L in summer 2009. Excluding station

K5 at the mouth of Arthur Kill, the stations in this region

averaged less than 10 ug/L Chlorophyll ‘a’. Raritan Bay

typically has high chlorophyll ‘a’ averages, thus the

proximity of K5 to the bay contributed to a rather high

summer average of 20.7 ug/L.

The Gowanus Canal station (G2) average chlorophyll ‘a’

decreased markedly from last year (14.5 ug/L), with an

average of 7.9 ug/L this summer. In mid-summer, some

individual samples can be as high as 38.8 ug/L, indicating

possible eutrophic conditions.

The Newtown Creek stations, which are not included

in the regional data, average chlorophyll ‘a’ between

23.9 ug/L at the mouth of the creek and 38.4 ug/L near

the head. This is typical of the creek and is likely a result

of nutrient enriched waters from runoff and minimal

tidal flushing.

T R E N D S

There is very little inter-annual chlorophyll ‘a’ variability

in the Inner Harbor. The summer averages here have

remained fairly constant and under 10.0 ug/L since 2000

(see figure). Massive water flow into the region from the

Hudson River has been thought to be a stabilizing factor,

keeping chlorophyll ‘a’ averages steady over the years.

Statue of Liberty as seen from DEP’s Harbor Survey Vessel Osprey.
2009 New York Harbor Water Quality Report

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SECCHI TRANSPARENCY

The Inner Harbor region encompasses many distinct

sub-regions: an estuary, a near fresh water river (Hudson

River), a narrow marine channel known to New Yorkers

as the “East River,” and an even narrower marine channel

(Arthur Kill) separating New Jersey and Staten Island that

is fed into by several smaller rivers and tributaries. It is

beneficial to consider these sub-regions separately.

In summer 2009, the average Secchi reading was 4.1 ft

in the Inner harbor area. Stations in the Staten Island

Kills and East River all averaged at least 4.2 ft, while

the Hudson River stations were all less than 3.0 ft. The

Hudson-Estuary area can be quite turbid from freshwater

influx and Secchi depths of 1.5 ft are quite common.

Newtown Creek also has low Secchi averages (all

stations <3.1 ft). A contributing factor seems to be

the high algal content discussed previously in the

Chlorophyll ‘a’ section.

T R E N D S

Average summer Secchi values have remained relatively

constant (>4.0 ft) in the Inner Harbor area since

measurements began in 1986, except in 1996 and 1997.

Compared with other city open waters, there have been

the least variations (<2.0 ft) over the past sampling years

(see figures). This can most likely be attributed to the

normal flow from the Hudson River.

Kayaking on Newtown Creek, with digester “eggs” in background

Harbor water sampling equipment aboard HSV Osprey
2009 New York Harbor Water Quality Report

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Upper East River –

Western Long Island Sound

FECAL COLIFORM

In 2009, water quality continued to be superior for

the Upper East River–Western Long Island Sound

(UER-WLIS). Fecal Coliform (FC) concentrations for all

monitoring sites except one at Flushing Creek (E15)

were in compliance with their specified “best use”

classifications for bathing and fishing. The summer

geometric mean for this region was 36 cells/100 mL,

up from 22 cells/100 mL in 2008. Eight of nine sites

had averages <40 cells/100 mL.

Enterococcus concentrations were also superior for the

area in 2009. The regional summer geometric mean was

5 cells/100 mL. All monitoring sites in the area complied

with the Bathing Standard of 35 cells/100 mL.

The Upper East River–Western Long

Island Sound (UER-WLIS) represents

the northeastern portion of NY Harbor,

from Hell Gate in the East River, up into

the Western Long Island Sound (WLIS).

The Harbor Survey Program provides

coverage of this area, including the

Harlem River and the East River, from

Roosevelt Island to Hart Island at the

NYC–Westchester County boundary.

This area contains nine Harbor Survey

monitoring stations. Waters of this

vicinity, though divergent in salinity and

depth, share similarities in pollutant

loadings and are targeted for intensive

management efforts as part of the Long

Island Sound National Estuary Program.

The majority of the Upper East River–

Western Long Island Sound complex is

classified as I, for uses such as fishing

or boating, with the area east of the

Bronx-Whitestone Bridge designated

for Bathing (SB).
2009 New York Harbor Water Quality Report

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DISSOLVED OXYGEN

T R E N D S

Fecal coliform (FC) concentrations have shown a

downward trend for more than twenty years in the

UER-WLIS region. The ongoing upgrade of wastewater

treatment facilities and capture of combined sewer

overflows (CSOs) were responsible for this FC reduction

and will continue to have a major impact on the

reduction of FC loads.

Enterococcus levels in the UER-WLIS have been

monitored since 2001. The averages for the past

years have been consistently well below the

Bathing Standard.

Average summer Dissolved Oxygen (DO) values for the

Upper East River and Western Long Island Sound (UERWLIS) vicinity met and exceeded 5.0 mg/L (conditions

suitable for SB-Bathing) in surface waters at 7 of 9 sites.

Average values for bottom waters at the three stations

designated as SB (stations E7, E8, and E10) were <0.5

mg/L below the 5.0 mg/L NYSDEC’s Bathing Standard.

However, they were all greater than last year’s averages

at these three stations.

Average DO levels stayed fairly consistent for the past

five years. Discrete DO measurements of surface and

bottom waters complied with the NYSDEC standards

74% and 66% of the time, respectively. It was 79% and

64% in 2008.

This year is the first time average bottom DO in the area

reached the Bathing Standard, since harbor survey

sampling began. Summer DO averaged 5.8 mg/L and 5.1

mg/L for surface and bottom waters; higher than the 5.6

mg/L and 4.8 mg/L in 2008.

Although average summer bottom DO was higher than

last year, incidents of hypoxia (DO <3.0 mg/L) were

measured at stations E7 (three times), E8 (six times) and

E10 (six times) from July 13th to August 31st. Consistent

with the past couple of years, minimum DO levels were

recorded in August.

T R E N D S

Average bottom DO values reached a record high in the

UER-WLIS area in summer 2009. For the first time,

average bottom DO was >5.0 mg/L which exceeded the

NYSDEC Bathing Standard. The trend analysis has shown

an increase in DO of about 1.0 mg/L for surface waters

and 1.5 mg/L for bottom waters. Most notable are

improvements in bottom waters that have risen from

below fishable (4.0 mg/L) in most of the 70s to above

the Bathing Standard in 2009. The trends also

demonstrate stability, with a decreasing gap between

surface and bottom waters, which occurred between

mid-1980s to early 2000s.

Mating blue crabs require brackish and ocean waters

to complete their life cycle
2009 New York Harbor Water Quality Report

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CHLOROPHYLL ‘a’

The stations in the Upper East River–Western Long

Island Sound (UER-WLIS) averaged below 20 ug/L of

chlorophyll ‘a’ in summer 2009. The highest averages

were found at E15 (18.2 ug/L) at the head of Flushing Bay

and E11 (19.0 ug/L) in Little Neck Bay. The head of

Flushing Bay, being adjacent to the mouth of Flushing

Creek, receives nutrient-rich water due to non-pointsource runoff in the creek. Other stations in the Upper

East River and Harlem River are typically low in average

chlorophyll ‘a’ (<5.6 ug/L). The overall average for the

entire region was 8.3 ug/L in summer 2009.

T R E N D S

Long-term trends for chlorophyll ‘a’ in this region show

summer averages in the 6-16 ug/L range dating back to

1986 (see figure). The two exceptions being 1995 and

1996, when concentrations averaged 22.8 ug/L and 25.8

ug/L, respectively. Furthermore, for the past eight years,

the summer averages have been less than 10 ug/L.

Upper East River –

Western Long Island Sound

DEP is now constructing nitrogen removal processes in

each of the four Upper East River Wastewater Treatment

Plants to reduce nutrient discharges.

The North River, one of three sludge vessels, in the East River
2009 New York Harbor Water Quality Report

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SECCHI TRANSPARENCY

In summer 2009, the average Secchi transparency for

Upper East River–Western Long Island Sound (UER-WLIS)

was 3.9 ft. Stations in more constricted waterways, such as

Flushing Creek Mouth (E15) and Harlem River (H3),

displayed low averages of less than 3.0 ft. Runoff after

rainfall can contribute to turbid waters in these areas.

T R E N D S

The UER-WLIS stations varied between 3.3 ft and 6.1 ft

Secchi depths since 1986. The lowest average Secchi

transparency of 3.3 ft in 1996 coincided with very high

average chlorophyll ‘a’ and total suspended solids

readings. Since 1996, improved Secchi transparency

depths may have coincided with decreased chlorophyll

‘a’ in this region. In 2009, however, the regional summer

average Secchi transparency dropped below 4.0 ft for

the first time since the low of 1996.

Bacteria filtration setup aboard the HSV Osprey

Kayaking at sunset on Jamaica Bay
2009 New York Harbor Water Quality Report

14

Jamaica Bay

CHLOROPHYLL ‘a’

Jamaica Bay is located at the southwestern end of Long Island. This urban,

estuarine embayment and national

park consists primarily of tidal wetlands,

upland areas and open waters. The

Bay and its drainage area are almost

entirely within the boroughs of Brooklyn

and Queens, except for a small area

at the eastern end that is in Nassau

County. Jamaica Bay joins the New York

Harbor to the west via the Rockaway

Inlet at the tip of Breezy Point and

includes the Rockaway Peninsula,

which forms the southern limit of the

Bay and separates it from the Atlantic

Ocean. This estuarine water body,

consisting of approximately 20 square

miles of open water, is covered by nine

Harbor Survey monitoring stations.

Open waters of Jamaica Bay are

classified for bathing or other

recreational use (SB). Areas within

the Bay’s tributaries and dead-end

canals are prone to reduced water

quality due to direct surface runoff

and poor flushing. These areas are

designated for secondary contact

use (I), such as fishing or boating.

FECAL COLIFORM

In 2009, sanitary water quality was superior for Jamaica

Bay, with summer fecal coliform (FC) concentrations

below 200 cells/100 mL, the Bathing Standard for all

stations, except Bergen Basin (J7).

Under wet weather conditions, the Bay experiences

localized degradation. At these times, spikes in FC may

temporarily exceed the Bathing Standard of 200

cells/100 mL for the entire northern portion of the Bay.

This decrease in water quality is limited to the Bay

proper, as Lower New York Bay waters are not typically

affected by wet weather events.

Enterococcus concentrations were also superior for

Jamaica Bay in 2009. The regional summer geometric

mean was 3 cells/100 mL; all monitoring sites complied

with the Bathing Standard of 35 cells/100 mL.
2009 New York Harbor Water Quality Report

15

T R E N D S

Average Fecal Coliform (FC) levels in Jamaica Bay have

been below the 200 cells/100 mL New York State

Standard for Bathing since 1985 except in 1990 when

it peaked at 210 cells/100 mL. The regional geometric

mean FC was 64 cells/100 mL in summer 2009.

The DEP continues to improve its sewage system

operations. Construction and operation of CSO

storage tanks continue in three Jamaica Bay tributaries.

Additionally, DEP skimmer vessels work to control

floatable debris in Jamaica Bay, as part of the “Boom

and Skim” program.

The 2009 summer averages for dissolved oxygen (DO)

for surface and bottom waters surpassed the New York

State Standard of never less than 5.0 mg/L for bathing

(SB) at all stations except for bottom waters at station

J12 (Grassy Bay).

Individual measurements comply with NYSDEC

Standards in 287 of 322 measurements. Most of the

lower DOs occurred at the northeastern part of Jamaica

Bay. At Bergen Basin (J7) and Spring Creek (J8), with

depths less than 30 ft, lower DO readings were found in

both surface and bottom waters during August and

September. At Grassy Bay (J12), 13 out of 18 bottom

samples measured during summer 2009 did not attain

the Bathing Standard; the bottom average DO was 4.1

mg/L. There were six (6) hypoxia events (DO <3.0 mg/L),

all recorded at Grassy Bay (J12). Lack of bottom water

circulation is the main issue at this 40 ft area.

DISSOLVED OXYGEN

T R E N D S

The regional average DO levels were well above the 5.0

mg/L Bathing Standard as early as 1970. DO variability is

high within and between years. The big gap (1.8 mg/L)

between surface and bottom waters has been reduced

since 2004. High surface DO levels are often due to

supersaturated conditions, attributable to algae blooms

and eutrophic waters. Also, pH average readings of 7.8 in

both surface and bottom waters were the highest within

the harbor area. Individual pH readings reached 8.72 in

surface water and 8.74 in bottom water.

Enterococcus levels in Jamaica Bay has been consistently

well below the Bathing Standard since 2001.

Yellow-crowned Night Heron in Jamaica Bay
2009 New York Harbor Water Quality Report

16

Jamaica Bay typically has the highest chlorophyll ‘a’

averages in all of the city’s marine waters. 2009 was

no exception, with an average of 37.7 ug/L. All stations

in the interior of the bay average over 35 ug/L, with

the higher averages being in the north-eastern side

of the bay (stations J7 and J12 chlorophyll ‘a’ averaged

around 50 ug/L). It is not uncommon for discrete

samples in the region to measure over 100 ug/L. Slow

turnover of water within the bay and the nutrient-rich

tributaries feeding it allow for development of large

standing phytoplankton populations.

At the mouth of Jamaica Bay (J1) and just outside the bay

(J11) chlorophyll ‘a’ concentrations were 19.8 ug/L and

14.9 ug/L, respectively. These areas receive some oceanic

water influx via Rockaway Inlet, resulting in lower

chlorophyll ‘a’ concentrations.

Jamaica Bay

CHLOROPHYLL ‘a’

Capital work at the 26th Ward Wastewater Treatment

Plant is ongoing to install process equipment that will

reduce nutrient discharges.

Floatables skimmer vessel in Hendrix Creek
2009 New York Harbor Water Quality Report

17

SECCHI TRANSPARENCY

T R E N D S

Inter-annual trends usually show higher chlorophyll ‘a’

readings in early summer, with levels settling down in

August and September. Although this was true for 2005

through 2008, because the early phytoplankton bloom

in the area was delayed in summer 2009, the monthly

chlorophyll ’a’ average peaked in August with 65.4 ug/L.

Over the past 24 years chlorophyll ‘a’ concentrations

have fluctuated rather wildly, particularly in the mid 90s.

The average Secchi transparency depth in Jamaica Bay was

3.7 ft in summer 2009. Two of the sample sites (J1 and J11)

are located outside the bay proper and experience greater

water exchange than sites within the bay. The Secchi

depth averages for these two sites were 5.7 ft and 4.7 ft,

respectively. In the interior of the bay, sample site Secchi

averages were very uniform (all about 3.3 ft).

T R E N D S

In Jamaica Bay, there is a loose correlation between

chlorophyll ‘a’ averages and water column Secchi

transparency. Average Secchi depths greater than 5.0 ft

were typical before 1993 when chlorophyll ‘a’ averages

were relatively low (see chlorophyll ‘a’ figure). Since that

time, the average Secchi transparency depths have been

between 3.3 ft and 4.4 ft.

Jamaica Bay Wildlife Refuge contains many diverse habitats,

including this freshwater pond

Large blooms cover Jamaica Bay’s Rosa rugosa

during the summer
2009 New York Harbor Water Quality Report

18

Lower New York Bay –

Raritan Bay

FECAL COLIFORM

The Lower NY Bay–Raritan Bay

(LNYB-RB) vicinity represents the most

oceanic portion of the Harbor Survey

Program. This area of 100 square miles

is represented by five Harbor Survey

monitoring stations and is composed

mostly of open shallow waters, partially

confined by Brooklyn’s Coney Island to

the north, Staten Island to the northwest,

and New Jersey’s Middlesex and

Monmouth counties and Sandy Hook

to the south. The remainder of its

eastern boundary is open to Rockaway

Inlet and the greater Atlantic Ocean.

This area of the harbor is classified for

bathing and other recreational use (SB).

Portions of those waters are also

designated for the permitted use of

shellfishing (for relay to cleaner waters,

but not direct consumption), having a

stricter use classification of SA.

In 2009, sanitary water quality as estimated by fecal

coliform (FC) had the lowest values in the Lower New

York Bay – Raritan Bay (LNYB-RB) as compared to other

waterbodies around New York City.

Summer averages for FC numbers show waters of the

LNYB-RB meet and surpass NYS Standards for this

area. Three of five stations had geometric means less

than 20 cells/100 mL (an order of magnitude below

State Standards).

In 2009, Enterococcus concentrations were the lowest

in the LNYB-RB compared to other waterbodies around

New York City. All stations’ averages were <3 cells/100 mL.
2009 New York Harbor Water Quality Report

19

DISSOLVED OXYGEN

T R E N D S

Fecal coliform (FC) concentrations for LNYB-RB show

significant decline from the mid-1980s to the present

time. While FC concentrations for surface waters were

always below 200 cells/100 mL, average FC levels

reached a low of 3 cells/100 mL in 1999. The levels have

remained at or below 11 cells/100 mL since then.

These improvements have allowed for the opening of all

NYC public beaches since 1992 and the lifting of wet

weather swimming advisories.

Enterococcus levels in the LNYB-RB have been

consistently well below the Bathing Standard.

Dissolved oxygen (DO) values for top and bottom waters

in Lower New York Bay – Raritan Bay (LNYB-RB) complied

with the NYS DO Standard of 5.0 mg/L for bathing waters

during the summer of 2009, except for three violations in

surface waters and seven in bottom waters. The ten

readings were within 3.8–4.8 mg/L, and 7 of 10 were

found at Raritan Bay (K5A). This is true despite K5A’s

proximity to more degraded waters in this region.

Summer average DO values in LNYB-RB have been the

highest among the harbor area since 2006. The average

DO measurements in summer 2009 were 7.6 mg/L in

surface waters and 7.0 mg/L in bottom waters, a slight

decrease from 8.3 mg/L and 7.8 mg/L in summer 2008.

T R E N D S

Average summer DO concentrations have increased

from 6.1 to 7.6 mg/L for surface waters, and from 5.2 to 7.0

mg/L for bottom waters from 1970 to 2009. Most of the

improvement in the LNYB-RB area is attributed to

improved water quality at station K5A. This improvement

reflects loading decreases of sanitary waste over the

years into Arthur Kill and the Raritan River.

School of Atlantic Silversides in Hendrix Creek

Great Egret over Jamaica Bay’s salt marsh
2009 New York Harbor Water Quality Report

20

CHLOROPHYLL ‘a’

This large region is represented by five Harbor Survey

stations. In the summer of 2009 the three stations on

the eastern side of this region (Lower Bay) typically had

low average chlorophyll ‘a’ concentrations (all <5.6 ug/L).

These waters are among the clearest in the city and are

represented by sampling stations at the Verrazano

Narrows (N8), Coney Island Beach (N9) and Rockaway

Point (N16). Conversely, the Raritan Bay stations on the

southeast shore of Staten Island have averages of 17.9

ug/L (K5A) and 25.5 ug/L (K6).

Raritan Bay appears to have a natural configuration ideal

for the promotion of phytoplankton blooms not only

in the summer, but in the winter as well. The relatively

shallow area’s main source of fresh water is the polluted

Raritan River. Flushing from the Hudson River is

inhibited by surrounding shoals, such as Old Orchard

Shoal. Tidal exchange with oceanic waters does occur,

but is inhibited somewhat by Sandy Hook.

Lower New York Bay –

Raritan Bay

DEP sludge vessel approaching the Verrazano-Narrows Bridge
2009 New York Harbor Water Quality Report

21

Lower Bay waters are generally very clear. An average of

6.4 ft this year reflects good transparency at open water

stations such as N16 at Rockaway Point (average of 9.4

ft) and N9 at Coney Island (8.3 ft). Levels above 5.0 ft

indicate clean conditions and superior water clarity.

Stations (K5A and K6) in Raritan Bay averaged lower <5.0

ft, as there are often phytoplankton blooms in the area

and turbid conditions on windy days.

T R E N D S

Average Secchi transparency readings in the Lower New

York Bay-Raritan Bay region have remained above 5.0 ft

since 1986, with the exceptions of 1995 and 1996. The

drop coincided with a large increase in chlorophyll ‘a’ in

1995 (see figure). Also within this time frame, the annual

Secchi averages fluctuated greatly, ranging from 4.4 ft to

almost 8.0 ft in just two years. It appears the region is

sensitive to annual variations that affect water clarity.

SECCHI TRANSPARENCY

T R E N D S

Given the propensity for algae blooms in Raritan Bay,

this region as a whole still has a history of having fairly

low summer chlorophyll ‘a’ averages. In fact, over the

past 24 years, all but three years (1995, 1997, 1998) had

averages below 20 ug/L (see figure). In 2009, the

chlorophyll ‘a’ average was 11.5 ug/L.

Common Tern with its next meal

Marine Sciences staff sampling in Gowanus Canal
2009 New York Harbor Water Quality Report

22

ater quality conditions in 2009 remained stable

or improved slightly. Harbor-wide average

Dissolved Oxygen (DO) values for both surface

and bottom waters remained at record highs, 6.8 mg/L

and 6.2 mg/L, respectively. Fecal Coliform (FC) and

Enterococci summer geometric means were well below

the New York State Department of Environmental

Conservation Standards for bathing and all recreational

use (200 cells/100mL for FC and 35 cells/100 mL for

Entero). Chlorophyll ‘a’, Secchi Depth and Total

Suspended Solids in the historical/open waters of the

harbor have remained stable with slight fluctuations.

For the first time on record, both surface and bottom

average DOs at all four regions exceeded 5.0 mg/L.

It was also the first time average bottom DO in the

UER-WLIS region reached a record high (5.1 mg/L).

Harbor-wide average DO levels at each sampling location

were all above the NYSDEC Bathing Standard of 5.0 mg/L,

except for a couple of areas in UER-WLIS and Grassy Bay

in Jamaica Bay (DOs between 4.1 mg/L and 4.9 mg/L).

It should be noted that this year’s bacterial geometric

means were reported slightly high because the estimated

‘Too Numerous to Count’ (TNTC) values were included in

the calculations.

Despite the inclusion of TNTC data, the harbor’s average

FC count remained stable at levels in compliance with

the Bathing Standard. All historical/open water stations

had average FC values well below the Bathing Standard,

except at Flushing Creek Mouth (E15) in UER-WLIS and

Bergen Basin (J7) in Jamaica Bay. Short-term spikes do

occur after rain events due to combined sewer overflow

(CSO) discharges.

Enterococcus sampling over the last nine years has

shown relatively stable average values, with spikes

similar in size and frequency to the fecal coliform levels.

As with the fecal averages, the enterococci averages for

the historical/open water sampling locations remain well

below the Bathing Standard (35 cells/100 mL). The NYC

DEP’s Long Term Control Plan (LTCP) is an ongoing

project which has begun addressing CSOs and

stormwater runoff.

In summer 2009, the harbor-wide chlorophyll ‘a’ average

remained at the same level as in 2008; Both surface and

bottom Total Suspended Solids and Secchi depth decreased.

The Harbor Survey has begun its integration into the

LTCP. Additional stations in the East River (Alley Creek)

and Jamaica Bay (Paerdegat Basin) have been added to

our regular sampling rotation in 2009.

Harbor-Wide Improvements

W
2009 New York Harbor Water Quality Report

23

Harbor-Wide Water Quality Improvements

Over Four Time Periods

NYS Best-Use Classifications: ≤200 FC/100 mL=SB (Bathing); ≤2000 FC/100 mL=I (Fishing).

NYC DOHMH requirements preclude bathing near sewer outfalls and where rainfall may substantially increase coliform levels.

SUMMER GEOMETRIC MEANS FOR

FECAL COLIFORM IN SURFACE WATERS

1985 1992

1999 2009
2009 New York Harbor Water Quality Report

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Harbor-Wide Water Quality Improvements

Over Four Time Periods

SUMMER AVERAGES FOR

DISSOLVED OXYGEN IN BOTTOM WATERS

NYS Best-Use Classifications: DO >5 mg/L=SB (Bathing); DO >4 mg/L=I (Fishing); DO >3 mg/L=SD (Fish Survival)

1985 1992

1999 2009
2009 New York Harbor Water Quality Report

25

Harbor-Wide Water Quality Improvements

Over Four Time Periods

SUMMER AVERAGES FOR

CHLOROPHYLL ‘a’ IN SURFACE WATERS

Chlorophyll ‘a’ >20 ug/L = Eutrophic conditions

1986 1992

1999 2009
2009 New York Harbor Water Quality Report

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2009 NYC DEP HARBOR SURVEY STATIONS
2009 New York Harbor Water Quality Report

27

NYC DEP WASTEWATER TREATMENT PLANTS AND CSOs
2009 New York Harbor Water Quality Report

28

Marine Section: Joseph Capiris, William Edgar,

Francisco Faundez, Jeffrey Ferenczy, Rudy Ferro,

Carl Jeremie, Michael Jonas, Christopher Lavin,

Mark Thomas and Brian Vaughan.

Wards Island Micro Lab: Personnel involved were

William Kelly, Paris Malakkhani, Claudette Williams,

Esmerado Castro, Naudet Joasil, Donnovon Johnson

and Alex Perez Padro.

This report was written by Naji Yao, Bernadette Boniecki

and Markus Koelbl. Edited by Naji Yao and Yin Ren.

Credits: Photos taken by Carl Ambrose and Scott Foster,

New York City DEP Photographers, and by Naji Yao,

Stavros Georgiadis and Markus Koelbl, Marine Sciences

Section, New York City DEP. Photos on pages 4, 7, 11,

13 (bottom), 15, 19 (bottom) and 21 (top) and cover,

courtesy of Don Riepe/Jamaica Bay Guardian.

he 2009 Harbor Survey Program was made

possible through the cooperative efforts of

the Marine Sciences Section, the Special Projects

Laboratory and the Marine Section of the New York

City Department of Environmental Protection’s Bureau

of Wastewater Treatment (BWT). The continued

development of the Harbor Survey Program is possible

by the dedication and professionalism of numerous staff

members from this Bureau, who are listed below.

Marine Sciences Section: Section Chief Beau Ranheim,

Bernadette Boniecki, Lloyd Stephen, Leela Maret,

Geneive Hall, William Lopez, Jiye Zhang, Stavros

Georgiadis, Markus Koelbl, Yin Ren and Naji Yao.

Fay Jacques and Veronica Rodriquez from the

Support Section also assisted.

Special Projects Laboratory: Supervised by

Trikan Patel and Patrick Jagessaar, with analyses

performed by: Lovely Chacko, Liji Isaac, Anna Chernyak,

Shyamlall Mahilall, Mohammed Ali, Shyla Ninan,

Piyush Patel and Carlos Quijije.

Acknowledgments

T

Printed on recycled paper

HSV Osprey working in Jamaica Bay

New York City Department of Environmental Protection

59-17 Junction Blvd., Flushing, NY 11373

Non-Emergency Help Call 311