Prepared in cooperation with the

Connecticut Department of Energy and Environmental Protection

Nutrient Concentrations and Loads and Escherichia coli

Densities in Tributaries of the Niantic River Estuary, 

Southeastern Connecticut, 2005 and 2008–2011

U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2013–5008
Cover. Photograph of the Niantic River, southeastern Connecticut, looking south toward Long Island Sound. The tributaries of 

Latimer Brook (right) and Oil Mill Brook (left) discharge to the estuary near the bottom of the photo. Courtesy of the Office of Long 

Island Sound Programs (OSLIP), Bureau of Water Protection and Land Reuse (WPLR), Connecticut Department of Energy and 

Environmental Protection (CT DEEP).
Nutrient Concentrations and Loads and 

Escherichia coli Densities in Tributaries 

of the Niantic River Estuary, Southeastern 

Connecticut, 2005 and 2008–2011

By John R. Mullaney

Prepared in cooperation with the Connecticut Department of Energy and 

Environmental Protection

Scientific Investigations Report 2013–5008

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013

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Suggested citation:

Mullaney, J.R., 2013, Nutrient concentrations and loads and Escherichia coli densities in tributaries of the Niantic 

River estuary, southeastern Connecticut, 2005 and 2008–2011: U.S. Geological Survey Scientific Investigations Report 

2013–5008, 27 p., http://pubs.usgs.gov/sir/2013/5008/.
iii

Acknowledgments

The author would like to thank the following individuals or groups for their assistance: Judy 

Rondeau and Patricia Young, Niantic River Watershed coordinators; the members of the Niantic 

River Watershed Committee; Kelly Streich, Eric Thomas, Stan Zaremba, and Paul Stacey, 

Connecticut Department of Energy and Environmental Protection; and Paul Corrente, Connecticut 

Department of Transportation. Timothy Frick, Joseph Martin, Guy Holzer, Nicholas Dosch, 

Michael Colombo, Jason Pollender, and Jonathan Morrison of the U.S. Geological Survey are 

acknowledged for data collection and analysis. Laura Medalie of the U.S. Geological Survey, 

and James Latimer of the U.S. Environmental Protection Agency are also thanked for providing 

technical review of this report.
This page has been left blank intentionally.
v

Contents

Abstract...........................................................................................................................................................1

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

Purpose and Scope ..............................................................................................................................3

Description of the Study Area ............................................................................................................3

Methods of Data Collection .........................................................................................................................4

Base Flow Survey in 2005....................................................................................................................4

Sampling of Tributaries From 2008 Through 2011 ............................................................................4

Streamflow Measurement ..................................................................................................................6

Water-Quality Field Measurement and Sampling Procedures .....................................................6

Laboratory Measurements..................................................................................................................6

Nutrient Load Calculation....................................................................................................................6

Nutrient Concentrations and Loads in Tributaries of the Niantic River Estuary .................................8

Watershed Base Flow Survey in 2005 ...............................................................................................8

Tributary Monitoring From 2008 Through 2011...............................................................................14

Streamflow..................................................................................................................................14

Nitrogen.......................................................................................................................................18

Phosphorus.................................................................................................................................20

Escherichia coli..........................................................................................................................20

Summary and Conclusions.........................................................................................................................22

Selected References...................................................................................................................................25

Figures

1. Map showing the Niantic River Basin in southeastern Connecticut...................................2

2. Map showing land use and land cover in the Niantic River Basin in 2006.........................5

3. Map showing nitrogen yields from selected basin segments in the Niantic River

Basin on June 1–3, 2005 ............................................................................................................13

4. Graph showing approximate compositional ranges of δ15N and δ18O data for

sources of nitrate........................................................................................................................14

5. Graph showing the instantaneous nitrogen yield by percentage of developed land

for basin segments in the Niantic River Basin from water-quality samples and

streamflow measurements collected June 1–3, 2005 ..........................................................15

6. Graphs showing daily discharge from A, Latimer Brook; B, Oil Mill Brook; C, Stony

Brook tributaries of the Niantic River, showing dates of samples collected, Niantic

River Basin, southeastern Connecticut ..................................................................................16

7. Boxplots showing the distribution of total nitrogen concentrations in the Niantic

River Basin in southeastern Connecticut from August 2008 through February 2012 ......18

8. Boxplots showing distribution of total ammonia plus organic nitrogen

concentrations in the Niantic River Basin in southeastern Connecticut from 

August 2008 through February 2012.........................................................................................20

9. Boxplots showing distribution of total phosphorus concentrations in the Niantic

River Basin in southeastern Connecticut from August 2008 through February 2012 ......22
vi

10. Boxplots showing distribution of Escherichia coli densities in the Niantic River

Basin in southeastern Connecticut from August 2008 through February 2012 ................24

11. Graphs showing cumulative probability plots of Escherichia coli densities for dry

and wet weather samples from October 2008 through September 2011 ..........................25

Tables

1. Land use in the Niantic River Basin in southeastern Connecticut in 2006 .........................7

2. Analytes for nutrient samples and analytical methods..........................................................8

3. Instantaneous nitrogen concentrations and loads, yields, and isotopic

measurements in the Niantic River Basin on June 1–3, 2005 ...............................................9

4. Streamflow and total nitrogen loads and yields for 11 basin segments in the 

Niantic River Basin on June 1–3, 2005 ....................................................................................10

5. Instantaneous phosphorus concentrations and loads and yields in the Niantic 

River Basin on June 1–3, 2005 ..................................................................................................12

6. Streamflow characteristics of three Niantic River tributaries in southeastern

Connecticut for water years 2009–2011..................................................................................15

7. Summary statistics of selected nitrogen and phosphorus constituents and

Escherichia coli for water-quality samples collected at three U.S. Geological 

Survey streamgages in the Niantic River Basin in southeastern Connecticut from 

August 2008 through February 2012.........................................................................................19

8. Loads and yields of total nitrogen and total ammonia plus organic nitrogen for 

three stations in the Niantic River Basin in southeastern Connecticut from 

October 2008 through September 2011 ...................................................................................21

9. Loads and yields of total phosphorus for three U.S. Geological Survey 

streamgages in the Niantic River Basin in southeastern Connecticut from 

October 2008 through September 2011 ...................................................................................23
vii

Conversion Factors and Datum

Multiply By To obtain

Length

foot (ft) 0.3048 meter (m)

Area

square mile (mi2

) 259.0 hectare (ha)

square mile (mi2

) 2.590 square kilometer (km2) 

Volume

million gallons (Mgal) 3,785 cubic meter (m3

)

cubic foot (ft3

) 0.02832 cubic meter (m3) 

Flow rate

cubic foot per second (ft3

/s) 0.02832 cubic meter per second (m3/s)

cubic foot per second per square 

mile [(ft3

/s)/mi2]

 0.01093 cubic meter per second per square 

kilometer [(m3/s)/km2]

million gallons per day (Mgal/d) 0.04381 cubic meter per second (m3

/s)

Mass

pounds per square mile per year 

[(lb/mi2

)yr]

0 .001751 kilogram per hectare per year 

[(kg/ha)/yr]

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

(NAVD 88).

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

Concentrations of chemical constituents in water are given in milligrams per liter (mg/L).

Abbreviations

AMLE adjusted maximum likelihood estimation

CTDEEP Connecticut Department of Energy and Environmental Protection

cfu colony-forming units

E. coli Escherichia coli

EWI equal width increment

LISS Long Island Sound study

LOADEST load estimator

MLE maximum likelihood estimation

NWIS National Water Information System

NWQL National Water Quality Laboratory 

USGS U.S. Geological Survey

USEPA U.S. Environmental Protection Agency
viii

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Nutrient Concentrations and Loads and Escherichia coli 

Densities in Tributaries of the Niantic River Estuary, 

Southeastern Connecticut, 2005 and 2008–2011

By John R. Mullaney

Abstract

Nutrient concentrations and loads and Escherichia 

coli (E. coli) densities were studied in 2005 and from 2008 

through 2011 in water-quality samples from tributaries of the 

Niantic River Estuary in southeastern Connecticut. Data from 

a water-quality survey of the base flow of subbasins in the 

watershed in June 2005 were used to determine the range of 

total nitrogen concentrations (0.09 to 2.4 milligrams per liter), 

instantaneous loads (less than 1 to 62 pounds per day) and 

the yields of total nitrogen ranging from 0.02 to 11.2 pounds 

per square mile per day (less than 1 to 7.2 kilograms per 

hectare per year) from basin segments. Nitrogen yields were 

positively correlated with the amount of developed land in 

each subbasin. Stable isotope measurements of nitrate (δ15N) 

and oxygen (δ18O) ranged from 3.9 to 9.4 per mil and 0.7 

to 4.1 per mil, respectively, indicating that likely sources of 

nitrate in base flow are soil nitrate and ammonium fertilizers, 

sewage or animal waste, or a mixture of these sources.

Continuous streamflow and monthly water-quality 

sampling, with additional storm event sampling, were 

conducted at the three major tributaries (Latimer Brook, 

Oil Mill Brook, and Stony Brook) of the Niantic River 

from October 2008 through September 2011. Samples 

were analyzed for nitrogen and phosphorus constituents 

and E. coli densities. Total freshwater discharge from these 

tributaries, which is reduced by upstream withdrawals, ranged 

from 25.9 to 37.8 million gallons per day. Total nitrogen 

and phosphorus concentrations generally were low, with 

the mean values below the U.S. Environmental Protection 

Agency recommended nutrient concentration values of 

0.71 milligram per liter and 0.031 milligram per liter, 

respectively. Total nitrogen was predominantly in the form of 

total ammonia plus organic nitrogen at the Oil Mill Brook and 

Stony Brook sites and in the form of nitrate at Latimer Brook.

Annual total nitrogen loads that flowed into the Niantic 

River estuary from the three major tributaries, calculated with 

the Load Estimator computer program, ranged from 41,400 

to 60,700 pounds, with about 52 to 59 percent of the load as 

total ammonia plus organic nitrogen. Total phosphorus loads 

ranged from 1,770 to 3,540 pounds per year. Yields of total 

nitrogen were highest from Latimer Brook, with the range 

from the three tributaries between 1,100 and 2,720 pounds per 

square mile per year. Total phosphorus yields ranged from 52 

to 185 pounds per square mile per year.

The geometric means of E. coli densities in samples 

from the three Niantic River tributaries were less than the 

State of Connecticut water-quality standard of 126 colonyforming units per 100 milliliters; however, individual samples 

from all three tributaries had densities as high as 2,400 to 

2,900 colony-forming units per 100 milliliters. High densities 

of E. coli were more likely to be present in samples collected 

during wet weather events.

Introduction

The Niantic River is an estuary at the mouth of a 

developed 30.2-square-mile (mi2

) coastal basin in southeastern 

Connecticut on Long Island Sound (fig. 1). The eelgrass beds 

of the Niantic River function as a nursery ground and feeding 

ground for a number of recreationally and commercially 

important bird, shellfish and finfish species. Many people 

enjoy the recreational opportunities afforded by the river, 

including boating, kayaking, sailing, swimming, fishing, and 

shellfishing. While the Niantic continues to serve all these 

functions, it has experienced fluctuations in water quality 

during the past few decades. The river once supported a major 

recreational scallop fishery, which has declined drastically. 

Episodic summertime hypoxia events in deeper bottom waters 

of the upper estuary have occurred occasionally. 

During the past two decades, point source nutrient loads 

associated with failing privately maintained onsite septic 

systems have been ameliorated along most of the developed 

shoreline of the Niantic River through the installation of 

municipal sewer systems. These controls have resulted 

in measurable improvements in the Niantic River. For 

example, eelgrass distribution and abundance have increased 

dramatically, and for the first time in more than two decades, 

winter 2011–12 was a very successful scallop season. 
2 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

East

Lyme

Montville

Waterford

Salem

Lyme

Old Lyme

New London

72°15' 72°10'

41°25'

41°20'

Niantic 

River

Niantic

Bay

Lake Konomoc

Latimer Brook

Oil Mill Brook

Stony Brook

Base from University of Connecticut, Department of Agriculture and Natural Resources, 2000

NAD83 Lambert Conformal Conic projection

0 1 2 MILES

0 1 2 KILOMETERS

01127791

01127786

01127778

011277918

011277916

011277913

011277905

011277875

011277795

011277914

0112779165

0112779135

4121480721223

CONNECTICUT

Niantic River 

Indian River Basin Long Island Sound

near Clinton

01195100

EXPLANATION

Continuous streamflow

and periodic water-quality 

site and number

Base flow water-quality survey 

site and number

Precipitation gage

and number

Basins upstream from continuous

 streamgages

Basin downstream from continuous

 streamgages

Basin boundary

Data collections site

Figure 1. The Niantic River Basin in southeastern Connecticut. The locations of U.S. Geological Survey (USGS) 

water-quality monitoring sites and streamgages in tributaries of the Niantic River Estuary are shown. NAD83, 

North American Datum of 1983.
Introduction 3

The presence of so-called “nuisance” macroalgae 

indicates that nitrogen loads are relatively high, though 

currently low enough to provide a suitable environment for 

eelgrass (Jamie Vaudrey, professor, University of Connecticut, 

written commun., April 2012). Excessive nitrogen loading 

to the Niantic River is considered to be a major cause of 

decline and variability of eelgrass populations (Connecticut 

Department of Environmental Protection, 2006). Currently, the 

Niantic River is the first embayment where eelgrass is present 

in Long Island Sound, when moving from west (New York 

City area) to east, along a gradient of improving water quality. 

Therefore, the Niantic River is currently thought to have 

marginal water quality with respect to eelgrass habitat. There 

is concern that, with increasing development in the watershed, 

the Niantic River will not be able to support eelgrass habitats 

in the future.

The Long Island Sound Study (LISS) began in 1985 

under the sponsorship of the U.S. Environmental Protection 

Agency (USEPA) and the States of Connecticut and New York 

to protect and restore the health of Long Island Sound.

The Connecticut Department of Energy and 

Environmental Protection (CTDEEP) and LISS are interested 

in improving eelgrass habitats and expanding the areas of 

suitable eelgrass habitat. In addition, research has been 

conducted to determine requirements to protect or improve 

eelgrass habitats in Long Island Sound (Vaudrey, 2008). 

The development of nutrient requirements for estuaries is 

complicated by the mixing of freshwater from tributaries 

and groundwater with saltwater from the ocean. The factors 

affecting optimal nutrient concentrations for eelgrass include 

the size of the watershed area relative to the area of the 

estuary, the volume of the tidal prism, the quality of marine 

water entering from outside the estuary, and additional factors.

The CTDEEP has listed the Niantic River on the impaired 

waters list of the State of Connecticut (Clean Water Act, secs. 

303b and 305b, 33 U.S.C. §§1313 and 1315); the river is 

considered to be impaired for habitat for marine fish, other 

aquatic life, and wildlife. The listed potential cause for this 

impairment includes eutrophication resulting from nutrients 

with sources such as flow alterations from water diversions, 

urban stormwater, on-vessel discharges, and residential land 

use (Connecticut Department of Environmental Protection, 

2011a, table 3–2).

The Niantic River also has been listed as impaired 

for shellfish harvesting due to the presence of excess 

fecal coliform bacteria, with sources ranging from urban 

stormwater, on-vessel discharges, onsite wastewater treatment 

systems, residential areas, and waterfowl. The lower reaches 

of the three major Niantic River tributaries also are listed as 

impaired by Escherichia coli (E. coli) bacteria (Connecticut 

Department of Environmental Protection, 2011a, table 3–2).

In 2006, the Niantic River watershed protection plan 

(Connecticut Department of Environmental Protection, 2006) 

was developed with recommendations to improve water 

quality throughout the watershed, eliminate shellfish bed 

closures, support fish and wildlife habitat, and provide safe 

and healthy recreational areas. Among the recommendations 

was monitoring of the Niantic River tributaries to provide 

baseline data on nutrients and bacteria to be compared 

with future conditions after management measures have 

been implemented.

An understanding of the river discharge and quantity 

and source of nutrients entering the Niantic River from the 

tributaries of the river is essential for establishing nutrient 

criteria for eelgrass survival. In addition, accurate information 

on the tributary loads of nutrients is required for understanding 

the mass balance and sources of nutrients in the watershed 

so the loads can be effectively managed. Data on indicator 

bacteria are necessary to provide baseline information to be 

compared with future data once management measures are in 

place to resolve the impairments.

To provide baseline data on the nutrient budget and the 

distribution of indicator bacteria, the U.S. Geological Survey 

(USGS) and the CTDEEP conducted cooperative studies in 

2005 and from 2008 through 2011 in the Niantic River Basin.

Purpose and Scope

This report provides information on the concentrations, 

loads, and yields of nitrogen and phosphorus in subbasins of 

the Niantic River. Data and data analysis are summarized from 

a basinwide base flow water-quality survey of nutrients from 

June 1–3, 2005, and includes nitrogen isotope composition of 

nitrate to assist with identifying sources of nitrogen. Data are 

presented on instantaneous streamflows and loads of nitrogen 

from 11 subbasins of the Niantic River.

The main focus of the report is on streamflow, nutrient, 

and indicator bacteria data from the three major tributaries 

of the Niantic River for the period October 2008 through 

February 2012. Data from this time period were used to 

develop statistical summaries of concentration and bacteria 

density. Data for water quality and streamflow from October 

2008 through September 2011 (water years1

 2009–2011) 

were used to calculate annual loads and yields of nitrogen 

and phosphorus.

Description of the Study Area

The Niantic River Basin is in coastal southeastern 

Connecticut, draining an area of 30.2 mi2

, and lies between the 

Connecticut River Basin on the west and the Thames River 

Basin on the east. The Niantic River estuary is primarily a 

saltwater environment that covers an area of 1.25 mi2

 at the 

mouth of the basin. The three largest tributaries contributing 

fresh water to the Niantic River estuary are Latimer Brook, Oil 

Mill Brook, and Stony Brook (fig. 1).

1

A water year is the period between October 1 of the previous year through 

September 30 of the year designated; for example, water year 2009 covers 

October 1, 2008, through September 30, 2009.
4 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

Land surface ranges from sea level near the mouth 

of the estuary to about 600 feet above the North American 

Vertical Datum of 1988 (NAVD88) in the headwaters in 

the town of Montville. Land cover and land use (University 

of Connecticut, 2009) in the watershed (fig. 2) is about 

61 percent forest, about 18 percent developed land, including 

turf, 5 percent wetlands, and 3.3 percent agricultural areas. 

The remaining 12.7 percent of the watershed contains areas 

with water, other grasses, barren land, and utility rights of 

way. About 12 percent of the watershed is in sewer service 

areas; not all areas within sewer service districts had sewers 

in 2012. Wastewater from the sewers is delivered to the 

sewage treatment system for the city of New London outside 

the Niantic River Basin and is discharged to the Thames 

River. The total population of the Niantic River Basin was 

about 8,500 in 2000 and 10,200 in 2010, based on a spatial 

analysis overlay of U.S. Census Bureau blocks with the basin 

boundaries (U.S. Census Bureau, 2012).

The surficial geology of the Niantic River Basin includes 

deposits of glacial till of varying thickness underlying 

75 percent of the watershed and coarse-grained glacial 

stratified deposits underlying 17 percent of the watershed, 

primarily in the river and stream valleys (Stone and others, 

1992). The remaining land area is underlain by fine-grained 

glaciolacustrine and swamp deposits. The surficial geology 

controls whether groundwater discharge or overland runoff is 

the dominant source of water and nutrients in different regions 

of the basin. Areas with coarse-grained glacial stratified 

deposits have higher groundwater recharge rates than areas 

with glacial till and consequently provide an important source 

of stream base flow (Thomas, 1966).

Methods of Data Collection

Data collected in June 2005 for the first phase of this 

project included surface water-quality samples that were 

collected, during typical base flows, and were analyzed 

for nitrogen concentrations. Instantaneous streamflow was 

measured at the time of sample collection to determine 

loads of nitrogen representative of groundwater discharge 

in selected parts of the Niantic River Basin. Data were used 

to determine which regions of the watershed had the largest 

yields of nitrogen. Water-quality samples were analyzed for 

nitrogen isotopes as a means identifying dominant sources of 

nitrate nitrogen.

For the second phase of the project, water-quality 

samples and continuous streamflow data were collected from 

2008 through 2012 at stations near the mouths of the three 

largest tributaries of the Niantic River—Latimer Brook, Oil 

Mill Brook, and Stony Brook. Samples were analyzed for 

concentrations of nutrients and densities of E. coli bacteria.

Base Flow Survey in 2005

A survey of base flow water quality was conducted in 

2005 to make initial estimates of the nutrient loads to Niantic 

River tributaries from groundwater discharge in different parts 

of the Niantic River Basin. Sites were selected at 11 locations 

(fig. 1; table 1) in the watershed for water-quality sampling 

and streamflow measurement.

Ideally, sampling would be designed to occur at a time 

when groundwater levels and stream base flows in the region 

were as close as possible to the long-term average. Data 

from the nearby long-term streamgage at the Indian River in 

Clinton (USGS streamgage 01195100; fig. 1, inset map) were 

examined to determine when conditions were similar to longterm average base flows. The base flow separation program 

PART (Rutledge, 1998) was used to analyze streamflow data 

from the Indian River streamgage collected from 1982 through 

2003 and estimate the long-term average base flow. The mean 

base flow from this period was estimated to be 6.6 cubic feet 

per second (ft3

/s). Samples were collected in the Niantic River 

Basin when the flow at the Indian River in Clinton was 3.0 to 

3.3 ft3

/s, indicating that base flows were about half the longterm average conditions. Therefore, loads estimated for this 

study may be lower than average.

Sampling was conducted during a dry 3-day period 

(June 1–3, 2005) to minimize change in streamflows during 

sampling. Samples were collected and analyzed for nitrogen 

and phosphorus constituents and for nitrogen 15-to-nitrogen 

14 ratio of nitrogen in nitrate (δ15N of NO3

) and oxygen 

18-to-oxygen 16 ratio of oxygen in nitrate (δ18O of NO3

). 

The nitrogen and oxygen isotopes were used to assist 

in determining the sources of nitrate in base flow to the 

tributaries of the basin.

Water-quality concentrations and instantaneous 

streamflow measurements were used to calculate instantaneous 

loads of total nitrogen and total phosphorus at each monitoring 

site. Load estimates were converted to estimates of nutrient 

yields to compare among subbasins. Loads for the watersheds 

of selected reaches were calculated by subtracting loads at 

the upstream monitoring sites from the loads at downstream 

locations. Yield was then calculated by dividing the 

instantaneous load (or gain in instantaneous load) by the 

drainage area in the selected reach.

Sampling of Tributaries From 2008 Through 2011

To determine continuous stream stage and discharge 

and to calculate the loads of nitrogen and phosphorus and 

densities of E. coli bacteria, streamgages were established 

on the three major tributaries of the Niantic River (fig. 1; 

table 1) during summer 2008. Water-quality samples were 

collected monthly at these sites and analyzed for nitrogen 

and phosphorus constituents and E. coli densities. Additional 
Methods of Data Collection 5

01127791

01127786

01127778

011277918

011277916

011277913

011277905

011277875

011277795

011277914

0112779165

0112779135

72°15' 72°10'

41°25'

41°20'

Niantic 

River

Niantic

Bay

Lake Konomoc

Latimer Brook

Oil Mill Brook

Stony Brook

4121480721223

Base from University of Connecticut, Department of Agriculture and Natural Resources, 2000

NAD83 Lambert Conformal Conic projection

Land use and land cover data from University of Connecticut, 2009,

Center for Land Use Education and Research

2

4

5

3 7

9

8

10

1

6

11

Continuous streamflow

and periodic water-quality 

site and number

Base flow water-quality survey 

site and number

Precipitation gage and

number

Developed

Turf and grass

Other grasses

Agriculture

Deciduous forest

Coniferous forest

Water

Nonforested wetland

Forested wetland

Barren land

Land use and land cover 2006

EXPLANATION

6 Basin or reach boundary and

number (table 4)

0 1 2 MILES

0 1 2 KILOMETERS

Figure 2. Land use and land cover in the Niantic River Basin, southeastern Connecticut, in 2006. NAD83, North American Datum 

of 1983; USGS, U.S. Geological Survey.
6 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

samples were collected during three storm and high-flow 

events in water years 2009 and 2010 to better define the 

relation between nutrient constituent concentrations and a 

range of streamflows. Annual loads of nutrient constituents 

were determined for water years 2009 through 2011. Field 

measurements of specific conductance, pH, dissolved oxygen, 

water temperature, and turbidity were made for every sample 

that was collected.

Streamflow Measurement

As part of the base flow water-quality survey, 

instantaneous streamflow measurements were made at selected 

sites in 2005. After the streamgages were established on 

Latimer Brook, Oil Mill Brook, and Stony Brook in 2008 

(fig. 1), streamflow measurements were made to develop 

and maintain stage-to-discharge rating curves for each site. 

Stage data were collected at 15-minute intervals at Latimer 

Brook and 5-minute intervals at Oil Mill Brook and Stony 

Brook. These stage data were used in conjunction with the 

rating curves to develop a record of continuous streamflow for 

each streamgage.

Streamflow measurements and discharge computations 

until 2010 were done following the procedures described in 

Rantz (1982a,b); after 2010, the methods were supplemented 

using techniques in Sauer and Turnipseed (2010) and 

Turnipseed and Sauer (2010).

Water-Quality Field Measurement and 

Sampling Procedures

Water-quality sample collection methods and equipment 

selection for this study are described in Wilde and others 

(1998a-c, 1999a,b). Sampling methods depended on the flow 

conditions. In high-flow conditions, samples were collected 

using an equal width increment (EWI) method, compositing 

samples from at least 10 equally spaced locations across 

the stream channel. In low-flow conditions, samples were 

collected using a single vertical in the channel thalweg. Field 

measurements were made during each site visit and included 

specific conductance, temperature, pH, dissolved oxygen, and 

turbidity. The methods are described in Wilde and Radtke 

(1998). Water-quality samples for nutrient analyses were 

preserved as needed and stored on ice before shipping within 

3 days to the USGS National Water Quality Laboratory 

(NWQL) in Denver, Colorado.

Water-quality samples also were collected from Latimer 

Brook, Oil Mill Brook, and Stony Brook to determine E. coli

bacteria densities. The samples were collected, processed, and 

analyzed by USGS field personnel using standard sampling 

procedures outlined by the Connecticut Department of 

Public Health and Connecticut Department of Environmental 

Protection (2003).

Laboratory Measurements

Table 2 lists the methods used to analyze samples for 

nitrogen and phosphorus species at the NWQL. Analytical 

results were entered into the National Water Information 

System (NWIS) database by laboratory personnel. Total 

nitrogen was calculated as the sum of total ammonia plus 

organic nitrogen and nitrite plus nitrate nitrogen.

Subsamples collected during the watershed base flow 

survey in 2005 also were analyzed for the δ15N of NO3

and δ18O of NO3

. Analysis for these isotopes required a 

concentration of at least 0.03 milligram per liter (mg/L) of 

nitrate as N and a total mass of 0.002 mg of nitrate as N in the 

sample. Samples were analyzed at the USGS Stable Isotope 

Laboratory in Reston, Virginia, using the methods in Coplen 

and others (2004).

Nutrient Load Calculation

Nutrient loads were calculated for data collected in 2005 

and from 2008 through 2011. Instantaneous nitrogen loads 

were calculated for the sites sampled during the 2005 base 

flow survey by multiplying the constituent concentration 

by the instantaneous flow and converting to appropriate 

units. Using data collected from 2008 through 2011, annual 

nutrient loads for nitrogen and phosphorus constituents were 

determined for the three Niantic River tributaries using the 

Load Estimator (LOADEST) computer program (Runkel and 

others, 2004). Given a time series of daily streamflow and 

instantaneous constituent concentration, LOADEST assists 

the user in developing a regression model for the estimation 

of constituent load. Explanatory variables in the regression 

model may include various functions of streamflow, decimal 

time, seasonal terms, and additional user-specified data. The 

formulated regression model then is used to estimate loads 

over a user-specified time interval.

Load estimations for this project used adjusted 

maximum likelihood estimation (AMLE; Cohn, 1988; 

Cohn and others, 1992) because the dataset contained 

censored data (below an analytical or reporting threshold). 

Retransformation bias (underestimation of true loads 

resulting from changing estimates made in log space back 

to actual numbers) is handled in the AMLE by equations 

specially designed for censored data. Load estimations using 

datasets with no censored data converge to the Maximum 

Likelihood Estimation (MLE); either estimation method, 

used appropriately, results in a minimum-variance, unbiased 

estimate of constituent loads (Runkel and others, 2004).

Estimations using the AMLE or MLE require that model 

residuals are normally distributed. As part of the evaluation of 

models, plots of residuals were analyzed graphically to verify 

that residuals met or nearly met normality assumptions.
Methods of Data Collection 

7

Table 1. Land use in the Niantic River Basin in southeastern Connecticut in 2006.[Land use and land cover is expressed as the percentage of watershed area covered by the land cover category. Land use and land cover data from University of Connecticut, 2009. ID, U.S. Geological Survey site identification number; s, base flow water-quality site, June 1–3, 2005; c, continuous streamflow and water-quality monitoring site for water years 2008 through 2011]

ID Latitude (° ʹ ′′) Longitude (° ʹ ′′) Drainage area, in mi2 Site type

Land use and land cover, in percent

Subbasin, site name Devel- oped Turf and grass

Agriculture 

and 

other 

grasses

Forest Water Wet- land

Barren 

land 

and

utility

Impervious 

cover 

in 2002

Latimer Brook

01127778 41°26ʹ39′′ 72°12ʹ09′′ 0.69 s Bogue Brook at Chesterfield Rd. near 

Chesterfield, Conn.

20.2 8.9 5.5 60.6 0.0 4.7 0.1 6.0

011277795 41°26ʹ20′′ 72°13ʹ25′′ 6.75 s Latimer Brook below Beckwith Pond near 

Chesterfield, Conn.

7.0 3.4 4.3 69.2 5.1 3.4 7.6 3.1

01127786 41°24ʹ18′′ 72°13ʹ33′′ 2.47 s Cranberry Meadow Brook at Rte. 161 near 

Chesterfield, Conn.

5.3 3.7 13.7 71.7 0.1 3.9 1.6 2.8

011277875 41°23ʹ51′′ 72°13ʹ22′′ 14.6 s Latimer Brook at Rocco Dr. near Chesterfield, 

Conn.

8.6 4.4 6.1 68.5 2.7 4.9 4.9 3.5

011277905 41°22ʹ07′′ 72°12ʹ08′′ 17.6 c, s Latimer Brook near I-95 N Exit 75 near 

Flanders, Conn.

10.5 4.6 6.2 66.6 2.8 4.6 4.7 3.9

Oil Mill Brook

01127791 41°24ʹ19′′ 72°10ʹ55′′ 2.15 s Lakes Pond Brook at State Rte. 85 near 

Chesterfield, Conn.

7.5 1.6 2.9 57.2 21.3 4.9 4.5 3.1

011277913 41°22ʹ51′′ 72°11ʹ15′′ 1.06 s Willys Meadow Brook at I-95 S near Flanders, 

Conn.

1.4 1.0 0.8 85.5 0.3 10.9 0.0 1.6

0112779135 41°22ʹ35′′ 72°11ʹ26′′ 5.37 s Oil Mill Brook near Oil Mill Rd. near Flanders, 

Conn.

9.9 2.2 3.4 66.1 8.7 6.9 2.8 3.6

011277914 41°22ʹ24′′ 72°11ʹ29′′ 5.67 c Oil Mill Brook at Gurley Rd. near East Lyme, 

Conn.

10.1 2.1 3.4 66.4 8.3 6.6 3.1 3.7

Stony Brook

011277916 41°21ʹ34′′ 72°10ʹ31′′ 1.86 c, s Stony Brook at Rte. 1 near Flanders, Conn. 15.3 2.3 8.1 61.9 0.2 9.5 2.6 5.8

Niantic River

0112779165 41°20ʹ00′′ 72°10ʹ24′′ 0.23 s Unnamed Brook at Niantic River Rd. near 

Graniteville, Conn.

32.7 10.2 0.2 46.1 3.4 7.1 0.3 11.3

011277918 41°19ʹ59′′ 72°11ʹ48′′ 0.31 s Unnamed Brook at Oswegatchie Hills Rd. near 

Niantic, Conn.

4.0 4.1 0.8 84.5 3.2 3.1 0.2 3.9
8 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

Table 2. Analytes for nutrient samples and analytical methods.

Analyte Reporting limit, 

in milligrams per liter Reference to methodology

Nitrogen, ammonia 0.01 Fishman (1993)

Nitrogen, ammonia plus organic, total 0.07 Patton and Truitt (2000)

Nitrogen, ammonia and organic, dissolved 0.07 Patton and Truitt (2000)

Nitrogen, nitrite 0.001 Fishman (1993)

Nitrogen, nitrite and nitrate 0.04 Patton and Kryskalla (2011), Fishman (1993)

Phosphorus, dissolved 0.003 U.S. Environmental Protection Agency (1993)

Phosphorus, phosphate, ortho 0.004 Fishman (1993)

Phosphorus, total 0.004 U.S. Environmental Protection Agency (1993)

Nutrient Concentrations and Loads in 

Tributaries of the Niantic River Estuary

Instantaneous loads of nutrients were calculated for 

11 monitoring stations sampled in June 2005, and isotopic 

analyses of nitrate were compared with known sources of 

nitrogen for 9 monitoring stations (table 3). Yields of nitrogen 

during the base flow survey were calculated for reaches of 

streams between monitoring stations in the Niantic River 

Basin and compared by differences in land use (table 4).

Data on nutrient concentrations and streamflows 

collected from August 2008 through February 2012 were 

analyzed to determine statistical distributions. They also were 

compared to USEPA recommended criteria for nitrogen and 

phosphorus concentrations in streams (U.S. Environmental 

Protection Agency, 2000). Annual loads and yields of total 

nitrogen and phosphorus, ammonia plus organic nitrogen, and 

dissolved phosphorus were calculated for water years 2009 

through 2011. E. coli densities were analyzed for waterquality samples collected from August 2008 through February 

2011 and compared with State of Connecticut water-quality 

standards. E. coli densities for samples collected from wet 

weather events and during dry weather for water years 2008 

through 2011 were compared.

Watershed Base Flow Survey in 2005

Instantaneous streamflow from the subbasins of the 

Niantic River during June 1–3, 2005, ranged from 0.09 

ft3

/s at Lakes Pond Brook (site 01127791; fig. 1) to 16 ft3/s 

at Latimer Brook (site 011277905; fig. 1; tables 3 and 5). 

Flows generally increased downstream; however, flows in 

Latimer Brook and Oil Mill Brook are probably lower than 

expected due to diversions from upstream reservoirs serving 

the city of New London. To understand the increase in flow 

due to groundwater discharge, gains in streamflow were 

calculated by subtracting the flows of upstream stations 

from downstream stations in the same subbasin. Gains in 

streamflow (table 4), which represent groundwater inflow, 

ranged from 0.04 to 2.25 cubic feet per second per square mile 

(ft3

/s/mi2; table 4) with the smallest discharge per unit area 

immediately downstream of reservoirs (site 01127791 at the 

outlet of Lake Konomoc). The largest discharge per unit area 

was measured in the lower part of the Oil Mill Brook Basin 

(basin segment 9; fig. 3). Gains in discharge per unit area 

were largest in segments dominated by coarse-grained glacial 

stratified deposits.

Total nitrogen concentrations ranged from 0.09 to 

2.4 mg/L (table 3). Total nitrogen concentrations included 

total ammonia plus organic nitrogen, which ranged from less 

than 0.09 to 0.27 mg/l, and nitrite plus nitrate nitrogen, which 

ranged from less than 0.06 to 2.0 mg/L. Samples from two 

locations did not have sufficient nitrate for isotopic analysis. 

Isotopic results for the remaining nine samples were overlain 

on a plot (fig. 4) of estimated compositions from different 

sources, including atmospheric deposition, synthetic nitrate 

fertilizers, soil nitrate and ammonium fertilizers, and sewage 

and animal wastes (Ging and others, 1996). Values of δ15N 

and δ18O in nitrate ranged from 3.92 to 9.43 per mil and 

0.74 to 4.1 per mil, respectively. Values from eight of the 

samples from the base flow survey plotted near the estimated 

compositions for soil nitrate and ammonium fertilizers, and 

one sample plotted within the range expected for sewage and 

animal wastes. Therefore, the likely sources of nitrogen from 

base flow samples in the Niantic River Basin are fertilizer, 

soil nitrate, and sewage or animal wastewater sources, or 

some combination. Samples from this survey do not show 

evidence of atmospheric sources or nitrate that has been 

subject to denitrification; nitrate from atmospheric deposition 

tends to have high values of δ18O, and samples showing 

denitrification would tend to have high values of δ18O and δ15N 

(Kendall, 1998).

Instantaneous total nitrogen loads (table 3) ranged 

from less than 1 to 62.1 pounds per day (lb/d) at the farthest 

downstream station on Latimer Brook (site 011277905). Total 

nitrogen loads at the farthest downstream stations on Oil Mill 

Brook (site 0112779135) and Stony Brook (site 011277916) 

were 11.1 lb/d and 6.9 lb/d, respectively. Instantaneous total 
Nutrient Concentrations and Loads in Tributaries of the Niantic River Estuary 9

Table 3. Instantaneous nitrogen concentrations, loads, yields, and isotopic measurements in the Niantic River Basin on June 1–3, 2005. [Land use and land cover is measured as a percentage of the area of each subbasin; ID, U.S. Geological Survey site identification number; ft3/s, cubic feet per second; mi2, square mile; N, nitrogen; mg/L, milligrams per liter; δ15N, ratio of nitrogen-15 to nitrogen-14 isotopes in nitrate; δ18O, ratio of oxygen-18 to oxygen-16 isotopes in nitrate; lb/d, pounds per day; kg/d, kilograms per day; lb/mi2/d, pounds per square 

mile per day; kg/ha/yr, kilograms per hectare per year; e, estimated; <, less than; --, nitrate concentrations insufficient for isotopic analysis]

ID Site name Date

Instantaneous 

discharge, 

in ft3/s

Drainage 

area, 

in mi2

Concentration

Total N, 

instantaneous 

load

Total N, 

instantaneous 

yield

Total 

ammonia 

plus 

organic N, 

in 

mg/L

Nitrite plus 

nitrate N, 

in 

mg/L

Total N, 

in 

mg/L

δ15N 

water, 

filtered, 

per mil

δ18O 

water, 

filtered, 

per mil

In 

lb/d

In 

kg/d

Converted 

to 

lb/mi2/d

Converted 

to 

kg/ha/yr

Latimer Brook

01127778 Bogue Brook at Chesterfield Rd. 

near Chesterfield, Conn.

6/2/2005 0.58 0.69 0.17 0.32 0.49 5.03 0.74 1.5 0.70 2.2 1.4

011277795 Latimer Brook below Beckwith 

Pond near Chesterfield, Conn.

6/2/2005 1.9 6.75 0.27 0.04e 0.31 3.92 3.50 3.2 1.44 0.47 0.30

01127786 Cranberry Meadow Brook at Rte. 

161 near Chesterfield, Conn.

6/2/2005 2.3 2.47 0.24 0.23 0.47 7.93 1.64 5.8 2.64 2.4 1.5

011277875 Latimer Brook at Rocco Dr. near 

Chesterfield, Conn.

6/2/2005 12 14.6 0.24 0.20 0.44 7.95 2.81 28.5 12.9 2.0 1.3

011277905 Latimer Brook near I-95 N Exit 75 

near Flanders, Conn.

6/2/2005 16 17.6 0.23 0.49 0.72 7.2 3.21 62.1 28.2 3.5 2.3

Oil Mill Brook

01127791 Lakes Pond Brook at State Rte. 85 

near Chesterfield, Conn.

6/3/2005 0.09 2.15 0.09e <0.06 0.09 -- -- 0.04 0.02 0.02 0.01

011277913 Willys Meadow Brook at I-95 S 

near Flanders, Conn.

6/1/2005 0.46 1.06 0.14 <0.06 0.14 -- -- 0.35 0.16 0.33 0.21

0112779135 Oil Mill Brook near Oil Mill Rd. 

near Flanders, Conn.

6/3/2005 5.4 5.37 0.21 0.17 0.38 7.47 2.14 11.1 5.0 2.1 1.3

Stony Brook

011277916 Stony Brook at Rte. 1 near 

Flanders, Conn.

6/1/2005 3.2 1.86 0.31 0.09 0.4 6.84 4.14 6.9 3.1 3.7 2.4

Niantic River

0112779165 Unnamed Brook at Niantic River 

Rd. near Graniteville, Conn.

6/1/2005 0.16 0.23 0.40 2.0 2.4 7.13 2.64 2.1 0.94 9.0 5.8

011277918 Unnamed Brook at Oswegatchie 

Hills Rd. near Niantic, Conn.

6/1/2005 0.17 0.31 0.28 0.24 0.52 9.43 4.10 0.48 0.22 1.5 0.98
10 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011 Table 4. Streamflow and total nitrogen loads and yields for 11 basin segments in the Niantic River Basin on June 1–3, 2005. [Map numbers are as they appear in figs. 2 and 3. Land use and land cover is measured as a percentage of the area of each subbasin or basin segment; -, minus; ft3/s, cubic feet per second; ft3/s/mi2, cubic feet per second per square mile; mi2, square mile; lb/d, pounds per day; kg/d, kilograms per day; lb/mi2/d, pounds per square mile per day; kg/ha/yr, kilograms per hectare per year] Map num- ber Subbasin and stations used in calculation Basin name, if separate basin Flow or difference in flow, in ft3/s Drainage area or difference in drainage area, in mi2 Flow/mi2 of basin segment in ft3/s/mi2 Total nitro- gen load or difference in nitrogen load Total nitrogen yield In lb/d In kg/d Converted to lb/mi2/d Converted to kg/ha/yr Latimer Brook

3 01127786 Cranberry Meadow Brook at Rte. 161 near 

Chesterfield, Conn.

2.3 2.47 0.93 5.8 2.6 2.4 1.5

4 011277875-(01127786+01127795) 7.8 5.38 1.45 19.5 8.8 3.6 2.35 011277905-011277875 4 3.00 1.33 33.7 15.3 11.2 7.2

Oil Mill Brook

1 01127778 Bogue Brook at Chesterfield Rd. near 

Chesterfield, Conn.

0.58 0.69 0.84 1.5 0.7 2.2 1.4

2 011277795-01127778 1.32 6.06 0.22 1.6 0.7 0.3 0.177 01127791 Lakes Pond Brook at State Rte. 85 near 

Chesterfield, Conn.

0.09 2.15 0.04 0.04 0.02 0.02 0.01

8 011277913 Willys Meadow Brook at I-95 S near Flanders, 

Conn.

0.46 1.06 0.43 0.3 0.2 0.3 0.21

9 0112779135-(011277913+01127791) 4.85 2.16 2.25 10.7 4.8 4.9 3.2

Stony Brook

10 011277916 Stony Brook at Rte. 1 near Flanders, Conn. 3.2 1.86 1.72 6.9 3.1 3.7 2.4

Niantic River

11 0112779165 Unnamed Brook at Niantic River Rd. near 

Graniteville, Conn.

0.16 0.23 0.70 2.1 0.9 9.0 5.8

6 011277918 Unnamed Brook at Oswegatchie Hills Rd. near 

Niantic, Conn.

0.17 0.31 0.55 0.5 0.2 1.5 0.98
Nutrient Concentrations and Loads in Tributaries of the Niantic River Estuary 11

Table 4. Streamflow and total nitrogen loads and yields for 11 basin segments in the Niantic River Basin on June 1–3, 2005.—Continued[Map numbers are as they appear in figs. 2 and 3. Land use and land cover is measured as a percentage of the area of each subbasin or basin segment; -, minus; ft3/s, cubic feet per second; ft3/s/mi2, cubic 

feet per second per square mile; mi2, square mile; lb/d, pounds per day; kg/d, kilograms per day; lb/mi2/d, pounds per square mile per day; kg/ha/yr, kilograms per hectare per year]

Map 

number

Subbasin and stations used 

in calculation Basin name, if separate basin

Land use and land cover, in percent

Deveoped

Turf 

and 

grass

Agriculture 

and 

other 

grasses

Forest Water Wetland

Barren 

land 

and 

utility

Impervious 

cover 

in 

2002

Latimer Brook

3 01127786 Cranberry Meadow Brook at Rte. 161 near 

Chesterfield, Conn.

5.3 3.7 13.7 71.7 0.1 3.9 1.6 2.8

4 011277875-(01127786+01127795) 12.0 5.8 4.9 66.3 0.8 7.1 3.0 4.2

5 011277905-011277875 20.0 5.5 6.7 57.3 3.5 3.3 3.7 6.0

Oil Mill Brook

1 01127778 Bogue Brook at Chesterfield Rd. near 

Chesterfield, Conn.

20.2 8.9 5.5 60.6 0.0 4.7 0.1 6.0

2 011277795-01127778 5.4 2.7 4.2 70.3 5.7 3.2 8.5 2.8

7 01127791 Lakes Pond Brook at State Rte. 85 near 

Chesterfield, Conn.

7.5 1.6 2.9 57.2 21.3 4.9 4.5 3.1

8 011277913 Willys Meadow Brook at I-95 S near Flanders, 

Conn.

1.4 1.0 0.8 85.5 0.3 10.9 0.0 1.6

9 0112779135-(011277913+01127791) 16.7 3.3 5.2 65.3 0.1 6.8 2.6 5.2

Stony Brook

10 011277916 Stony Brook at Rte. 1 near Flanders, Conn. 15.3 2.3 8.1 61.9 0.2 9.5 2.6 5.8

Niantic River

11 0112779165 Unnamed Brook at Niantic River Rd. near 

Graniteville, Conn.

32.7 10.2 0.2 46.1 3.4 7.1 0.3 11.3

6 011277918 Unnamed Brook at Oswegatchie Hills Rd. near 

Niantic, Conn.

4.0 4.1 0.8 84.5 3.2 3.1 0.2 3.9
12 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011 Table 5. Instantaneous phosphorus concentrations, loads and yields in the Niantic River Basin on June 1–3, 2005. [ID, U.S. Geological Survey site identification number; ft3/s, cubic feet per second; mi2, square miles; mg/L, milligrams per liter; P, phosphorus; lb/d, pounds per day; kg/d, kilograms per day; lb/mi2/d, pounds per square mile per day; kg/ha/yr, kilograms per hectare per year; e, estimated; <, less than; na, load calculation not possible due to phosphorus concentrations less than the reporting limit] ID Site name Date sampled Instanta- neous discharge, in ft3/s Drainage area, in mi2 Concentration Total P, instantaneous load Total P, instantaneous yield Phosphorus, dissolved, in mg/L Total P, in mg/L In lb/d In kg/d Converted to lb/mi2/d Converted to kg/ha/yr Latimer Brook 01127778 Bogue Brook at Chesterfield Rd. near Chesterfield, Conn. 6/2/2005 0.58 0.69 0.005 0.015 0.047 0.021 0.068 0.04 011277795 Latimer Brook below Beckwith Pond near Chesterfield, Conn. 6/2/2005 1.9 6.75 0.004 0.020e 0.205 0.093 0.030 0.02 01127786 Cranberry Meadow Brook at Rte. 161 near Chesterfield, Conn. 6/2/2005 2.3 2.47 0.010 0.017 0.211 0.096 0.085 0.05 011277875 Latimer Brook at Rocco Dr. near Chesterfield, Conn. 6/2/2005 12 14.6 0.006 0.016 1.04 0.470 0.071 0.05 011277905 Latimer Brook near I-95 N Exit 75 near Flanders, Conn. 6/2/2005 16 17.6 .004e 0.014 1.21 0.548 0.069 0.04 Oil Mill Brook 01127791 Lakes Pond Brook at State Rte. 85 near Chesterfield, Conn. 6/3/2005 0.09 2.15 0.004 <0.008 na na na na 011277913 Willys Meadow Brook at I-95 S near Flanders, Conn. 6/1/2005 0.46 1.06 0.006 <0.006 na na na na 0112779135 Oil Mill Brook near Oil Mill Rd. near Flanders, Conn. 6/3/2005 5.4 5.37 0.006 0.011 0.320 0.145 0.060 0.04 Stony Brook 011277916 Stony Brook at Rte. 1 near Flanders, Conn. 6/1/2005 3.2 1.86 0.009 0.017 0.293 0.133 0.158 0.10 Niantic River 0112779165 Unnamed Brook at Niantic River Rd. near Graniteville, Conn. 6/1/2005 0.16 0.23 0.019 0.040 0.035 0.016 0.150 0.10 011277918 Unnamed Brook at Oswegatchie Hills Rd. near Niantic, Conn. 6/1/2005 0.17 0.31 0.006 0.011 0.010 0.005 0.033 0.02
Nutrient Concentrations and Loads in Tributaries of the Niantic River Estuary 13

2

4

5

3 7

9

8

10

1

6

72°15' 72°10'

41°25'

41°20'

Lake Konomoc

Base from University of Connecticut, Department of Agriculture and Natural Resources, 2000

NAD83 Lambert Conformal Conic projection

11

01127786 01127791

01127778

011277918

011277916

011277795

0112779165

Latimer Brook

Oil Mill Brook

Stony Brook

011277905

Niantic 

River

011277913

0112779135

EXPLANATION

Instantaneous nitrogen yield,

 in kg/ha/yr

0.013 - 0.17

>0.17 - 0.98

>0.98 - 1.51

>1.51 - 2.93

>2.93 - 7.17

Base flow water-quality survey 

site and number

6 Basin or reach boundary and

number (table 4)

0 1 2 MILES

0 1 2 KILOMETERS

Niantic

Bay

Figure 3. Nitrogen yields from selected basin segments in the Niantic River Basin, southeastern Connecticut, on June 1–3, 2005. 

kg/ha/, (kilograms per hectare per year); NAD83, North American Datum of 1983; USGS, U.S. Geological Survey.
14 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

USGS base flow water-quality

site and identification number

0112779135

-10

0

10

20

30

40

50

60

70

80

-5 0 5 10 15 20 25

Atmospheric

sources

Synthetic nitrate

fertilizers

Soil nitrate

and ammonium

fertilizers

Sewage and animal wastes

Areas of overlap

δ15N of nitrate, in per mil

δ18O of nitrate, in per mil

EXPLANATION

01127778 011277795 011277918

01127786

011277875

0112779135

011277916

011277905

0112779135

Figure 4. Approximate compositional ranges of δ15N and δ18O data for sources of nitrate. Reproduced from Ging 

and others (1996). Water-quality samples collected June 1–3, 2005, from the Niantic River Basin, southeastern 

Connecticut, are plotted. δ15N, ratio of nitrogen-15 to nitrogen-14 isotopes of nitrate; δ18O, ratio of oxygen-18 to 

oxygen-16 isotopes of nitrate; USGS, U.S. Geological Survey.

nitrogen yields also were calculated as gains by river reach, by 

subtracting the upstream loads from the loads at downstream 

stations and dividing by the drainage area of the reach 

(table 4).

Total nitrogen yields from basins or basin segments 

ranged from 0.02 to 11.2 pounds per square mile per 

day (lb/mi2

/d; 0.01 to 7.2 kilograms per hectare per year 

(kg/ha/yr); tables 3 and 4). The highest yield was measured 

for the segment between stations 011277905 and 011277875 

on Latimer Brook (fig. 3, segment 5) and was due to an 

increase of 33.7 lb/d [15.3 kilograms per day (kg/d)] in total 

nitrogen load (table 4). The next largest yield, 9.0 lb/mi2

/d 

(5.8 kg/ha/yr), was from an unnamed brook (station 

0112779165; fig. 3, segment 11). Total nitrogen yields were 

positively correlated with the percentage of developed land 

use for each basin segment (fig. 5).

Sources of nitrogen in base flow are generally 

representative of the quality of groundwater discharging to 

the stream; the isotopic measurements from the water-quality 

samples analyzed indicate the possibility of elevated nitrogen 

from fertilizers and septic systems or some mixture of sources, 

including soil nitrate. These samples only represent base flow, 

and therefore, samples collected during stormwater runoff 

events may have different sources of nitrogen.

Instantaneous total phosphorus concentrations were 

generally low, ranging from less than 0.006 to 0.040 mg/L. 

Instantaneous total phosphorus loads ranged from 0.010 to 

1.21 lb/d at the farthest downstream station on Latimer Brook 

(site 011277905). Total phosphorus loads from the farthest 

downstream stations on Oil Mill Brook (site 0112779135) and 

Stony Brook (site 011277916) were 0.320 lb/d and 0.293 lb/d, 

respectively, representing the base flow load of phosphorus to 

the estuary (table 5). Total phosphorus instantaneous yields 

ranged from 0.033 to 0.158 lb/mi2

/d (0.02 to 0.1 kg/ha/yr).

Tributary Monitoring From 2008 Through 2011

Streamflow

Streamflow was greatest during water year 2010 

(table 6, fig. 6) due to extreme high flows caused by excessive 

rainfall that occurred around March 30, 2010, when a total 

of 9.2 inches of rainfall was measured at USGS rain gage 

4121480721223 (fig. 1) in East Lyme. Although this was 

an extreme event that affected the mean flows for that year, 

median flows were highest in water year 2009.
Nutrient Concentrations and Loads in Tributaries of the Niantic River Estuary 15

0 10 20 30

Developed land, in percent

0

2

4

6

Instantaneous yield,

converted to kilograms per hectare per year

40

8

11

5

1

10

9

4

3

6

8 2 7

Yield (= 0.1955 x percent developed) - 0.2153

adjusted R2

= 0.57

EXPLANATION

Basin and number—locations

shown in figures 2 and 3

11

Figure 5. Instantaneous nitrogen yield by percentage of 

developed land for basin segments in the Niantic River Basin from 

water-quality samples and streamflow measurements collected 

June 1–3, 2005. R2

, coefficient of determination.

Table 6. Streamflow characteristics of three Niantic River tributaries in southeastern Connecticut for water years 2009–2011.

[ID, U.S. Geological Survey site identification number; mi2, square mile; ft3/s, cubic feet per second; max., maximum; min., minimum]

ID Site name

Drainage 

area, 

in mi2

Minimum, 

in ft3

/s

Lower 

quartile, 

in ft3

/s

Median, 

in ft3

/s

Mean, 

in ft3/s

Upper 

quartile, 

in ft3

/s

Maximum, 

in ft3

/s

Runoff,

in 

inches

Water year 2009

011277905 Latimer Brook near I-95 N Exit 75 near 

Flanders, Conn.

17.6 2.8 16.0 29.0 36.0 41.0 462 27.8

011277914 Oil Mill Brook at Gurley Rd. near East 

Lyme, Conn.

5.67 1.6 4.5 7.0 8.5 10.0 92 20.4

011277916 Stony Brook at Rte. 1 near Flanders, Conn. 1.86 0.48 2.0 3.8 4.5 5.3 56 33.0

Water year 2010

011277905 Latimer Brook near I-95 N Exit 75 near 

Flanders, Conn.

17.6 1.2 8.9 20.0 43.3 42.0 1,350 33.4

011277914 Oil Mill Brook at Gurley Rd. near East 

Lyme, Conn.

5.67 0.98 2.9 5.9 9.7 10.0 330 23.2

011277916 Stony Brook at Rte. 1 near Flanders, Conn. 1.86 0.41 1.2 3.0 5.6 5.4 194 40.7

Water year 2011

011277905 Latimer Brook near I-95 N Exit 75 near 

Flanders, Conn.

17.6 2.1 9.2 16.0 28.3 32.0 266 21.8

011277914 Oil Mill Brook at Gurley Rd. near East 

Lyme, Conn.

5.67 1.5 3.1 7.0 8.0 10.0 54 19.2

011277916 Stony Brook at Rte. 1 near Flanders, Conn. 1.86 0.5 1.4 2.3 3.7 4.3 30 27.3
16 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

1

10

100

1,000

Discharge, in cubic feet per second

A. Latimer Brook

0.1

1

10

100

1,000

10/1/08

1/1/094/1/097/1/09

10/1/09

1/1/11

10/1/10

1/1/104/1/107/1/104/1/11

10/1/11

7/1/11

Date

B. Oil Mill Brook

Daily mean discharge

Water-quality sample collection

EXPLANATION

Daily mean discharge

Water-quality sample collection

EXPLANATION

Figure 6. Daily discharge from A, Latimer Brook; B, Oil Mill Brook; C, Stony Brook tributaries of the 

Niantic River, showing dates of samples collected, Niantic River Basin, southeastern Connecticut.
Nutrient Concentrations and Loads in Tributaries of the Niantic River Estuary 17

0

1

10

100

1,000

Discharge, in cubic feet per second

10/1/08

1/1/094/1/097/1/09

10/1/09

1/1/11

10/1/10

1/1/104/1/107/1/104/1/11

10/1/11

7/1/11

Date

C. Stony Brook

Daily mean discharge

Water-quality sample collection

EXPLANATION

Figure 6. Daily discharge from A, Latimer Brook; B, Oil Mill Brook; C, Stony Brook tributaries 

of the Niantic River, showing dates of samples collected, Niantic River Basin, southeastern 

Connecticut.—Continued

The total mean daily flow from the three major 

tributaries with continuous streamflow ranged from 40 ft3

/s 

(25.9 million gallons per day (Mgal/d)) in water year 2011 to 

58.6 ft3

/s (37.8 Mgal/d) in water year 2010.

The annual total runoff (the part of precipitation 

appearing in surface streams) from each of the watersheds 

was variable. Stony Brook had the greatest amount of runoff 

ranging from 27.3 inches in water year 2011 to 40.7 inches 

in water year 2010. The other two sites had lower runoff for 

each of the three water years likely due to water diversions 

from reservoirs in the Latimer Brook and Oil Mill Brook 

Basins. If runoff from Stony Brook (which has no reservoirs) 

is representative of the amount of natural runoff for the 

region, then the difference between the runoff from Oil Mill 

Brook and Latimer Brook relative to Stony Brook should 

be generally representative of the amount of water diverted 

out of the Niantic Basin (assuming change in storage in the 

reservoirs is negligible). The total difference in runoff between 

Stony Brook and the other two tributaries (Oil Mill Brook 

and Latimer Brook) ranged from 10.5 to 16.9 ft3

/s (7.8 to 

10.9 Mgal/d), indicating that flows to the Niantic River have 

been altered substantially by diversion. The estimated demand 

for water from users in the city of New London for 2010 was 

expected to be 5.9 Mgal/d, based on projections in the regional 

water supply plan (Southeastern Connecticut Water Authority, 

2003). Differences between the estimated diversions and the 

calculated differences among tributaries described above 

may be attributed to (1) the assumption that runoff from 

Stony Brook is representative of prediversion runoff from the 

other stations; (2) changes in surface water storage; (3) small 

errors in measurement of watershed area or streamflow; or 

(4) diversions of water that were larger than those projected in 

the water supply plan of 2003.

The diversion of water from the Niantic River likely 

affects the nutrient cycling of the downstream estuary by 

(1) reducing the overall loading rate of nutrients that originate 

upstream of the water diversion and (2) increasing the 

freshwater residence time of the estuary. Nutrient loads are 

reduced, but the freshwater that remains in the estuary is likely 

to reside in the estuary for a longer time period. The remaining 

nutrients have not been diluted by the lower concentrations of 

nutrients that would have originated in the forested watersheds 

upstream of water supply diversions. 
18 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

Nitrogen

Concentrations of total nitrogen (fig. 7; table 7) were 

generally low at all three stations relative to many locations 

in Connecticut. The highest concentrations of total nitrogen 

were in samples from the Latimer Brook site, whereas Oil 

Mill Brook and Stony Brook had similar distributions of 

concentration for samples collected from 2008 through 

2012 (fig. 7). Latimer Brook had higher concentrations of 

total nitrogen than did Oil Mill Brook and Stony Brook, 

which had similar distributions of concentration for samples 

collected from 2008 through 2012 (fig.7; table7). The median 

concentrations of total nitrogen at these three sites were lower 

than the median value of 0.67 mg/L of data from 38 stations 

on streams draining to Long Island Sound.

The mean value of total nitrogen was 0.42 mg/L for 

Oil Mill Brook and Stony Brook and 0.62 mg/L for Latimer 

Brook. These mean total nitrogen concentrations are below 

the 0.71 mg/L USEPA ecoregion XIV (Eastern Coastal Plain) 

total nitrogen recommended criterion for streams (U.S. 

Environmental Protection Agency, 2000).

Concentrations of total ammonia plus organic nitrogen 

ranged from less 0.07 to 0.93 mg/L (fig. 8; table 7). Ammonia 

plus organic nitrogen typically represented less than 

50 percent of the total nitrogen concentrations at the Latimer 

Brook site, but represented more than 50 percent of the total 

nitrogen concentrations in samples from the Oil Mill Brook 

and Stony Brook sites. Concentrations of dissolved ammonia 

typically represented less than 10 percent of the total ammonia 

plus organic nitrogen, indicating that organic nitrogen is 

dominant species.

Total nitrogen loads for all three Niantic River tributaries 

combined for water years 2009 through 2011 ranged from 

41,400 to 60,700 lb (table 8). Total nitrogen loads were 

consistent with drainage area with the largest loads from 

Latimer Brook, followed by Oil Mill Brook and Stony Brook. 

The largest loads were estimated for water year 2010, likely 

caused at least in part by the additional runoff associated with 

the storm of March 30, 2010.

Loads of total ammonia plus organic nitrogen (table 8) 

for all three Niantic River tributaries combined ranged from 

22,000 lb in water year 2011 to 35,600 lb in water year 

2010. Total ammonia plus organic nitrogen represented 52 

to 59 percent of the load of total nitrogen from the three 

Niantic River tributaries. Loads of total ammonia plus organic 

nitrogen were largest relative to loads of total nitrogen at 

Oil Mill Brook and Stony Brook, representing more than 

60 percent of the load of total nitrogen and as much as 

80 percent of the load for Stony Brook in 2010.

Total nitrogen yields (table 8) were generally highest at 

Latimer Brook, followed by Stony Brook and Oil Mill Brook. 

The total nitrogen yields at all three tributaries are generally 

39

EXPLANATION 

Number of values

75th percentile

Largest value within 1.5 times

interquartile range above

75th percentile 

25th percentile

Interquartile

range 

x Outside value—Value is greater

than 1.5 and less than 3 times

the interquartile range

beyond either end of the box

50th percentile

(median)

Smallest value within 1.5 times

interquartile range below

25th percentile

x

x

x

x

x

011277905 011277914 011277916

0.2

0.4

0.6

0.8

1.0

1.2

51 51 51

Total nitrogen

USGS steamgage

Concentration, in milligrams per liter

Figure 7. Distribution of total nitrogen concentrations in the Niantic River Basin in southeastern Connecticut from 

August 2008 through February 2012. Data shown are from U.S. Geological Survey (USGS) streamgages 011277905 at 

Latimer Brook, 011277914 at Oil Mill Brook, and 011277916 at Stony Brook. Line represents the median of samples from 

38 stations in the Long Island Sound watershed from October 1995-September 2009.
Nutrient Concentrations and Loads in Tributaries of the Niantic River Estuary 19

Table 7. Summary statistics of selected nitrogen and phosphorus constituents and Escherichia coli for water-quality samples collected at three U.S. Geological Survey 

streamgages in the Niantic River Basin in southeastern Connecticut from August 2008 through February 2012.

[Concentrations in milligrams per liter; ID, U.S. Geological Survey site identification number; cfu, colony forming units; e, estimated; >, greater than; <, less than; E. coli, Escherichia coli; --, not applicable]

ID Streamgage Constituent

Number 

of 

samples

Minimum Mean 25th percentile Median 75th percentile Maximum Geometric mean

Milligrams per liter

011277905 Latimer Brook near I-95 N Exit 75 near Flanders, Conn. Nitrogen, total 51 0.41 0.62 0.48 0.56 0.77 1.00 --011277914 Oil Mill Brook at Gurley Rd. near East Lyme, Conn. Nitrogen, total 51 0.24 0.42 0.33 0.40 0.48 0.86 --011277916 Stony Brook at Rte. 1 near Flanders, Conn. Nitrogen, total 51 0.22 0.42 0.30 0.39 0.48 0.98 --011277905 Latimer Brook near I-95 N Exit 75 near Flanders, Conn. Ammonia nitrogen, dissolved 51 <0.01 0.02 0.01 0.02 0.02 0.030 --011277914 Oil Mill Brook at Gurley Rd. near East Lyme, Conn. Ammonia nitrogen, dissolved 51 e0.01 0.02 0.01 0.02 0.02 0.065 --011277916 Stony Brook at Rte. 1 near Flanders, Conn. Ammonia nitrogen, dissolved 51 <0.01 0.02 0.01 0.02 0.02 0.089 --011277905 Latimer Brook near I-95 N Exit 75 near Flanders, Conn. Ammonia plus organic nitrogen, dissolved 51 0.09 0.23 0.16 0.23 0.26 0.42 --011277914 Oil Mill Brook at Gurley Rd. near East Lyme, Conn. Ammonia plus organic nitrogen, dissolved 51 0.09 0.22 0.16 0.18 0.26 0.50 --011277916 Stony Brook at Rte. 1 near Flanders, Conn. Ammonia plus organic nitrogen, dissolved 51 0.07 0.27 0.17 0.26 0.32 0.58 --011277905 Latimer Brook near I-95 N Exit 75 near Flanders, Conn. Ammonia plus organic nitrogen, total 51 0.08 0.27 0.17 0.25 0.32 0.72 --011277914 Oil Mill Brook at Gurley Rd. near East Lyme, Conn. Ammonia plus organic nitrogen, total 51 0.08 0.26 0.17 0.20 0.29 0.77 --011277916 Stony Brook at Rte. 1 near Flanders, Conn. Ammonia plus organic nitrogen, total 51 0.07 0.30 0.18 0.27 0.37 0.93 --011277905 Latimer Brook near I-95 N Exit 75 near Flanders, Conn. Nitrite plus nitrate nitrogen, dissolved 51 0.05 0.35 0.21 0.33 0.51 0.71 --011277914 Oil Mill Brook at Gurley Rd. near East Lyme, Conn. Nitrite plus nitrate nitrogen, dissolved 51 <0.02 0.16 0.09 0.17 0.22 0.32 --011277916 Stony Brook at Rte. 1 near Flanders, Conn. Nitrite plus nitrate nitrogen, dissolved 51 <0.02 0.11 0.05 0.10 0.14 0.31 --011277905 Latimer Brook near I-95 N Exit 75 near Flanders, Conn. Phosphorus, dissolved 50 <0.003 0.008 0.005 0.007 0.01 0.025 --011277914 Oil Mill Brook at Gurley Rd. near East Lyme, Conn. Phosphorus, dissolved 50 0.003 0.009 0.005 0.008 0.01 0.021 --011277916 Stony Brook at Rte. 1 near Flanders, Conn. Phosphorus, dissolved 50 <0.003 0.011 0.006 0.011 0.02 0.034 --011277905 Latimer Brook near I-95 N Exit 75 near Flanders, Conn. Phosphorus, total 50 e0.006 0.021 0.009 0.014 0.02 0.11 --011277914 Oil Mill Brook at Gurley Rd. near East Lyme, Conn. Phosphorus, total 50 e0.004 0.021 0.008 0.012 0.02 0.13 --011277916 Stony Brook at Rte. 1 near Flanders, Conn. Phosphorus, total 50 e0.004 0.024 0.013 0.018 0.03 0.15 --

Colony forming units per 100 milliliter

011277905 Latimer Brook near I-95 N Exit 75 near Flanders, Conn. E. coli 51 1 278 23 59 180 > 2,400 63

011277914 Oil Mill Brook at Gurley Rd. near East Lyme, Conn. E. coli 51 2 213 9 26 120 e2,900 36011277916 Stony Brook at Rte. 1 near Flanders, Conn. E. coli 51 1 300 16 42 290 2,800 62
20 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

51

EXPLANATION 

Number of values

75th percentile

Largest value within 1.5 times

interquartile range above

75th percentile 

25th percentile

Interquartile

range 

x Outside value—Value is greater

than 1.5 and less than 3 times

the interquartile range

beyond either end of the box

Far-out value—Value is equal or

greater than 3 times the

interquartile range beyond

either end of box

50th percentile

(median)

Smallest value within 1.5 times

interquartile range below

25th percentile

o

x

x

x

x

x

x

o

o

x

x

011277905 011277914 011277916

0.0

0.2

0.4

0.6

0.8

1.0

1.2

51 51 51

Total ammonia plus organic nitrogen

USGS streamgage

Concentration, in milligrams per liter

Figure 8. Distribution of total ammonia plus organic nitrogen concentrations in the Niantic River Basin in southeastern Connecticut 

from August 2008 through February 2012. Data shown are from U.S. Geological Survey (USGS) streamgages 011277905 at Latimer 

Brook, 011277914 at Oil Mill Brook, and 011277916 at Stony Brook.

representative of loads from forested basins, although total 

nitrogen yields from Latimer Brook are slightly higher than 

the maximum 2,000 lb/mi2

/yr for forested basins reported by 

Trench (2000). Yields of total nitrogen may be lowest at Oil 

Mill Brook because of the lowest amount of developed and 

agricultural land of the three basins (table 1). Nitrogen loads 

and yields at Oil Mill Brook and Latimer Brook are likely less 

than they would be under natural flow conditions because of 

the large diversions of water upstream from the streamgages. 

Stony Brook had the highest yield of total ammonia plus 

organic nitrogen.

Phosphorus

Total phosphorus concentrations in most samples were 

low in all three tributaries of the Niantic River, ranging 

from less than 0.004 to 0.15 mg/L; dissolved phosphorus 

concentrations ranged from less than 0.003 mg/L to 

0.034 mg/L (fig. 9, table 7). Most samples were below the 

0.031-mg/L USEPA total phosphorus criterion for streams for 

ecoregion XIV (U.S. Environmental Protection Agency, 2000). 

Dissolved phosphorus typically was less than 50 percent of 

the total phosphorus in samples from Latimer Brook and Oil 

Mill Brook, but represented more than 50 percent of total 

phosphorus in Stony Brook. Selected statistics on phosphorus 

concentrations are in table 7.

The total phosphorus loads (table 9) from all three 

Niantic River tributaries ranged from 1,770 lb in water year 

2011 to 3,540 lb in water year 2010. Latimer Brook accounted 

for 72 to 75 percent of the total phosphorus load from the 

three tributaries; Oil Mill Brook and Stony Brook, 16 to 

16.6 percent and 9.7 to 11 percent, respectively.

Total phosphorus yields were highest at Stony Brook, 

followed by Latimer Brook and Oil Mill Brook. Yields ranged 

from a low of 52 lb/mi2

/yr at Oil Mill Brook in water year 

2011 to 185 lb/mi2

/yr at Stony Brook in water year 2010. 

Yields of total phosphorus from Latimer Brook and Oil Mill 

Brook are likely also lower than would be expected without 

water diversions from the upper watershed.

Escherichia coli

The geometric mean values of E. coli densities at the 

three sampling stations from August 2008 through February 

2012 (table 7) meet the Connecticut water-quality standard 

of less than 126 colony-forming units (cfu) per 100 milliliters 

(mL) for all forms of water recreation (Connecticut 

Department of Energy and Environmental Protection, 2011b). 

All three monitoring stations had single sample maximum 

densities in excess of the 235 cfu per 100 mL, 410 cfu per 

100 mL, and 576 cfu per 100 mL standards for designated 

swimming, nondesignated swimming, and other water 
Nutrient Concentrations and Loads in Tributaries of the Niantic River Estuary 21

Table 8. Loads and yields of total nitrogen and total ammonia plus organic nitrogen for three stations in the Niantic River Basin in 

southeastern Connecticut from October 2008 through September 2011.

[ID, U.S. Geological Survey site identification number; lb/d, pounds per day; lb/yr, pounds per year; lb, pounds; lb/mi2/yr, pounds per square mile per year; 

kg/ha/yr, kilograms per hectare per year]

ID Site name Water 

year

Flux, 

in 

lb/d

Lower limit 

of the 95th 

percent 

confidence 

interval, 

in lb/yr

Upper limit 

of the 95th 

percent 

confidence 

interval, 

in lb/yr

Annual 

load, 

in 

lb

Annual 

yields, 

in 

lb/mi2

/yr

Annual 

yields, 

in 

kg/ha/

yr

Total nitrogen

011277905 Latimer Brook near I-95 N Exit 75 near 

Flanders, Conn.

2009 111.0 37,700 43,400 40,400 2,300 4.03

011277905 2010 131.0 43,500 52,800 48,000 2,720 4.76

011277905 2011 88.3 30,100 34,500 32,200 1,830 3.20

011277914 Oil Mill Brook at Gurley Rd. near East 

Lyme, Conn.

2009 19.4 6,580 7,630 7,090 1,250 2.19

011277914 2010 21.7 7,150 8,760 7,920 1,400 2.45

011277914 2011 17.2 5,840 6,719 6,270 1,100 1.93

011277916 Stony Brook at Rte. 1 near Flanders, Conn. 2009 9.6 3,220 3,780 3,490 1,880 3.29

011277916 2010 13.0 4,250 5,320 4,760 2,560 4.48

011277916 2011 8.0 2,720 3,170 2,940 1,580 2.77

Total load from tributaries 2009 51,000

2010 60,700

2011 41,400

Total ammonia plus organic nitrogen

011277905 Latimer Brook near I-95 N Exit 75 near 

Flanders, Conn.

2009 51.8 16,100 22,100 18,900 1,070 1.87

011277905 2010 71.9 21,400 31,800 26,200 1,490 2.61

011277905 2011 43.2 13,600 18,200 15,800 896 1.57

011277914 Oil Mill Brook at Gurley Rd. near East 

Lyme, Conn.

2009 12.9 4,200 5,290 4,730 830 1.45

011277914 2010 15.2 4,670 6,540 5,540 980 1.72

011277914 2011 10.5 3,500 4,220 3,850 680 1.19

011277916 Stony Brook at Rte. 1 near Flanders, Conn. 2009 7.7 2,530 3,100 2,800 1,510 2.64

011277916 2010 10.5 3,220 4,510 3,830 2,060 3.61

011277916 2011 6.4 2,110 2,560 2,330 1,250 2.19

Total load from tributaries 2009 26,400

2010 35,600

2011 22,000
22 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

50

EXPLANATION 

Number of values

75th percentile

Largest value within 1.5 times

interquartile range above

75th percentile 

25th percentile

Interquartile

range 

x Outside value—Value is greater

than 1.5 and less than 3 times

the interquartile range

beyond either end of the box

Far-out value—Value is equal or

greater than 3 times the

interquartile range beyond

either end of box

50th percentile

(median)

Smallest value within 1.5 times

interquartile range below

25th percentile

x

x

xx

o

oo

o

x

x

o

o

o

o

o

o

011277905 011277914 011277916

0.0

0.02

0.06

0.10

0.14

0.18

50 50 50

Total phosphorus

USGS streamgage

Concentration, in milligrams per liter

o

Figure 9. Distribution of total phosphorus concentrations in the Niantic River Basin in southeastern Connecticut from August 2008 

through February 2012. Data shown are from U.S. Geological Survey (USGS) streamgages 011277905 at Latimer Brook, 011277914 at 

Oil Mill Brook, and 011277916 at Stony Brook.

recreation, respectively (table 7). A Kruskal-Wallis multiple 

comparison test determined that the distributions of E. coli

densities were not significantly different among water-quality 

samples from the three tributaries (fig. 10).

Wet weather samples (stormflow) were separated from 

base flow samples for each station by using the base flow 

separation program PART (Rutledge, 1998) to classify samples 

as base flow versus storm runoff. Samples collected on days 

when at least 80 percent of the flow was base flow were 

considered to be dry weather samples, and samples from days 

when more than 20 percent of the flow was from stormwater 

runoff were classified as wet weather samples. Samples of 

each type (dry and wet) were plotted on cumulative probability 

plots for comparison of the E. coli distributions (fig. 11A–C). 

Wet weather samples at all three sites had a higher probability 

of exceeding Connecticut water-quality standards. The source 

of these elevated E. coli densities is likely stormwater runoff.

Summary and Conclusions

A study of the concentrations and loads of nitrogen and 

phosphorus and the densities of Escherichia coli (E. coli) 

bacteria in the Niantic River Basin was conducted by the 

U.S. Geological Survey (USGS) in cooperation with the 

Connecticut Department of Energy and Environmental 

Protection in June 2005 and from 2008 through 2011. High 

nitrogen loads from the Niantic River Basin have the potential 

to adversely affect eelgrass growth and survival in the Niantic 

River. Eelgrass is an important habitat for finfish and shellfish. 

In addition, several downstream reaches of streams in the 

Niantic River Basin are impaired because of E. coli densities 

that exceed State of Connecticut water-quality standards.

Land use in the Niantic River Basin is dominated by 

forested land; about 21 percent of the land in the watershed 

has been developed for residential, commercial, or agricultural 

uses. The surficial geology of the basin is dominated by glacial 

till deposits. Glacial stratified deposits are present in about 

17 percent of the watershed and are an important source of 

base flow to Niantic River tributaries and the Niantic River.

Water-quality sampling was conducted in subbasins of 

the watershed at 11 locations in June 2005 as part of a base 

flow water-quality survey to determine the distribution of 

nutrient loads from groundwater to Niantic River tributaries. 

Samples were analyzed for nitrogen and phosphorus 

constituents and nitrogen and oxygen isotopes of nitrate in 

order to identify potential sources of nitrogen.

Concentrations of total nitrogen during this base flow 

survey ranged from 0.09 to 2.4 milligrams per liter (mg/L). 

Values of δ15N and δ18O in nitrate ranged from 3.92 to 

9.43 per mil and 0.74 to 4.10 per mil, respectively. The 

combinations indicated that the sources of nitrate in most 

samples are fertilizer or soil nitrate, sewage or animal waste, 

or a mixture of two or more sources. Instantaneous loads of 

total nitrogen ranged from 0.04 to 62.1 pounds per day (lb/d), 
Summary and Conclusions 23

Table 9. Loads and yields of total and dissolved phosphorus for three U.S. Geological Survey streamgages in the Niantic River Basin 

in southeastern Connecticut from October 2008 through September 2011.

[ID, U.S. Geological Survey site identification number; lb/d, pounds per day; lb/yr, pounds per year; lb, pounds; lb/mi2/yr, pounds per square mile per year; 

kg/ha/yr, kilograms per hectare per year]

ID Site name Water 

year

Flux, 

in lb/d

Lower limit 

of the 95th 

percent 

confidence 

interval, 

in lb/yr

Upper limit 

of the 95th 

percent 

confidence 

interval, 

in lb/yr

Annual 

load, 

in lb

Annual 

yields, 

in lb/

mi2

/yr

Annual 

yields, 

in kg/

ha/yr

Total phosphorus

011277905 Latimer Brook near I-95 N Exit 75 near 

Flanders, Conn.

2009 3.9 1,100 1,810 1,420 81 0.14

011277905 2010 7.3 1,790 3,780 2,650 151 0.26

011277905 2011 3.5 1,020 1,580 1,280 73 0.13

011277914 Oil Mill Brook at Gurley Rd. near East 

Lyme, Conn.

2009 0.8 220 416 307 54 0.09

011277914 2010 1.5 282 941 540 95 0.17

011277914 2011 0.8 224 380 295 52 0.09

011277916 Stony Brook at Rte. 1 near Flanders, Conn. 2009 0.5 152 234 190 102 0.18

011277916 2010 0.9 237 486 345 185 0.32

011277916 2011 0.5 159 238 196 105 0.18

Total load from tributaries 2009 1,920

2010 3,540

2011 1,770

Dissolved phosphorus

011277905 Latimer Brook near I-95 N Exit 75 near 

Flanders, Conn.

2009 1.7 546 702 620 35 0.06

011277905 2010 1.9 577 849 703 40 0.07

011277905 2011 1.4 436 559 495 28 0.05

011277914 Oil Mill Brook at Gurley Rd. near East 

Lyme, Conn.

2009 0.4 136 171 153 27 0.05

011277914 2010 0.4 131 175 152 27 0.05

011277914 2011 0.3 114 139 126 22 0.04

011277916 Stony Brook at Rte. 1 near Flanders, Conn. 2009 0.3 87 115 100 54 0.09

011277916 2010 0.3 83 115 98 53 0.09

011277916 2011 0.2 77 102 89 48 0.08

Total load from tributaries 2009 870

2010 950

2011 710
24 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

51

EXPLANATION 

Number of values

75th percentile

Largest value within 1.5 times

interquartile range above

75th percentile 

25th percentile

Interquartile

range 

x Outside value—Value is greater

than 1.5 and less than 3 times

the interquartile range

beyond either end of the box

Far-out value—Value is equal or

greater than 3 times the

interquartile range beyond

either end of box

50th percentile

(median)

Smallest value within 1.5 times

interquartile range below

25th percentile

o

x

o

o

o

o

xx

o

o

o

o

o

x

o

o

o

o

011277905 011277914 011277916 0

500

1,000

1,500

2,000

2,500

3,000

3,500

51 51 51

USGS streamgage

Escherichia coli

Colony forming units per 100 milliliters

Figure 10. Distribution of Escherichia coli densities in the Niantic River Basin in southeastern Connecticut from August 2008 

through February 2012. Data shown are from U.S. Geological Survey (USGS) streamgages 011277905 at Latimer Brook, 011277914 

at Oil Mill Brook, and 011277916 at Stony Brook.

with the largest load from the farthest downstream site on 

Latimer Brook. Nitrogen yields from basin segments were 

calculated as the difference between downstream and upstream 

sites divided by the difference in drainage area. Instantaneous 

total nitrogen yields ranged from 0.02 to 11.2 pounds per 

square mile per day (lb/mi2

/d; less than 0.01 to 7.2 kilograms 

per hectare per year (kg/ha/yr)). The largest instantaneous 

yields were measured on the farthest downstream reach of 

Latimer Brook (between two monitoring stations) and from a 

small unnamed tributary of the Niantic River that discharges 

on the southeastern side of the river. The yields measured 

were generally positively correlated with the percentage of 

developed land in the drainage area to each reach.

Instantaneous total phosphorus concentrations measured 

during the base flow survey were generally low, ranging from 

less than 0.006 to 0.040 mg/L; instantaneous total phosphorus 

loads ranged from less than 0.010 to 1.20 lb/d.

Beginning in August 2008, streamgages were installed 

at the downstream end of the three major tributaries of the 

Niantic River—Latimer Brook, Oil Mill Brook, and Stony 

Brook. Samples analyzed for nitrogen and phosphorus 

constituents and for E. coli bacteria collected monthly (with 

additional stormflow samples) from August 2008 to February 

2012 were used in the analysis in this report.

The total mean daily flow from all three Niantic River 

tributaries measured at the streamgages ranged from 25.9 

to 37.8 million gallons per day (Mgal/d). The runoff from 

the Stony Brook site was greater than that from Oil Mill 

Brook and Latimer Brook likely due to diversions of water 

for public water supply from the headwaters of these basins. 

The difference in runoff (converted to streamflow) between 

Stony Brook and Oil Mill Brook and Latimer Brook combined 

is equivalent to 7.8 to 10.9 Mgal/d, which is more than the 

estimated water diversions from the Oil Mill Brook and 

Latimer Brook Basins. Withdrawal of water from the Niantic 

River Basin may affect the cycling and delivery of nutrients to 

the estuary.

Total nitrogen concentrations were generally low at 

all three tributary monitoring stations, with mean values 

below the 0.71-mg/L U.S. Environmental Protection Agency 

(USEPA) recommended nitrogen criterion. Samples from 

Latimer Brook had higher concentrations of total nitrogen 

than Oil Mill Brook and Stony Brook, but all concentrations 

measured were at or less than 1 mg/L. Total ammonia 

plus organic nitrogen was more than 50 percent of the 

total nitrogen in samples from Oil Mill Brook and Stony 

Brook. Organic nitrogen was the dominant species in total 

ammonia plus organic nitrogen analyses of samples from all 

three tributaries.

Total nitrogen loads for water years 2009 through 2011 

ranged from 41,400 to 60,700 lb combined for all three 

Niantic River tributaries, with the largest loads during water 

year 2010. The largest loads were from Latimer Brook and 

represented 78 to 80 percent of the total nitrogen load from the 

three tributaries. Loads of total ammonia plus organic nitrogen 

ranged from 22,000 to 35,600 lb and represented 52 to 

60 percent of the total nitrogen load from the three tributaries. 

The total nitrogen load from Stony Brook was dominated by 
Selected References 25

1 50 100 500 1,000

0

0.2

0.4

0.6

0.8

1.0

Cumulative probability

A. Latimer Brook

Escherichia coli, in colony forming units per 100 milliliters

Dry weather, 28 samples

Wet weather, 16 samples

EXPLANATION

105

Dry weather, 31 samples

Wet weather, 13 samples

EXPLANATION

0.0

0.2

0.4

0.6

0.8

1.0

Cumulative probability

Escherichia coli, in colony forming units per 100 milliliters

B. Oil Mill Brook

1 105 50 100 500 1,000

Dry weather, 29 samples

Wet weather, 15 samples

EXPLANATION

1 105 50 100 500 1,000

0.0

0.2

0.4

0.6

0.8

1.0

Cumulative probability

Escherichia coli, in colony forming units per 100 milliliters

C. Stony Brook

Figure 11. Cumulative probability plots of Escherichia coli

densities for dry and wet weather samples from October 

2008 through September 2011. Data from U.S. Geological 

Survey (USGS) streamgages A, 011277905 at Latimer Brook, B,

011277914 at Oil Mill Brook, and C, 011277916 at Stony Brook are 

shown.

total ammonia plus organic nitrogen. Total nitrogen yields 

ranged from 1,100 lb/mi2/yr at Oil Mill Brook in water year 

2011 to 2,720 lb/mi2/yr at Latimer Brook in water year 2010. 

Total nitrogen yields were generally within the range for 

other forested basins in New England; Latimer Brook had the 

highest yields.

Total phosphorus concentrations ranged from less than 

0.004 to 0.15 mg/L, and mean concentrations from all three 

stations were less than the mg/L USEPA recommended 

nutrient criterion for ecoregion XIV. Total phosphorus loads 

from the three stations totaled 1,770 to 3,540 pounds per year 

(lb/yr), with yields ranging from 53 to 187 lb/mi2

/yr.

The geometric means of E. coli densities in samples 

from the three Niantic River tributaries were less than State of 

Connecticut water-quality standards. Single samples from all 

three stations had densities that exceeded the single-sample 

maximum values for the State’s water-quality standards. An 

analysis of E. coli densities by sample type (wet weather 

versus base flow) indicated that wet weather (stormflow) 

samples were more likely to exceed the State’s waterquality standards.

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26 Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011

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Mullaney—Nutrient Concentrations and Loads and E. coli densities, Niantic River, Southeastern Connecticut, 2005 and 2008–2011—Scientific Investigations Report 2013–5008