National Water Quality Program

Design and Methods of the U.S. Geological Survey Northeast 

Stream Quality Assessment (NESQA), 2016

Open-File Report 2018–1183

U.S. Department of the Interior

U.S. Geological Survey
Cover. Map of the Northeast Stream Quality Assessment study area, modified from figure 2A of this report.
Design and Methods of the U.S. Geological 

Survey Northeast Stream Quality 

Assessment (NESQA), 2016

By James F. Coles, Karen Riva-Murray, Peter C. Van Metre, Daniel T. Button, 

Amanda H. Bell, Sharon L. Qi, Celeste A. Journey, and Richard W. Sheibley

National Water Quality Program

Open-File Report 2018–1183

U.S. Department of the Interior

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

DAVID BERNHARDT, Acting Secretary

U.S. Geological Survey

James F. Reilly II, Director

U.S. Geological Survey, Reston, Virginia: 2019

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Suggested citation:

Coles, J.F., Riva-Murray, K., Van Metre, P.C., Button, D.T., Bell, A.H., Qi, S.L., Journey, C.A., and Sheibley, R.W., 2019, 

Design and methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016: U.S. 

Geological Survey Open-File Report 2018–1183, 46 p., https://doi.org/10.3133/ofr20181183.

ISSN 2331-1258 (online)
iii

Contents

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

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

Background............................................................................................................................................2

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

Study Area Description........................................................................................................................3

Study Design...................................................................................................................................................6

Site Selection.........................................................................................................................................6

Land-Use Designations........................................................................................................................7

Sample Collection and Processing.............................................................................................................7

Comprehensive Stream Water Data................................................................................................10

Discrete Water-Quality Samples.............................................................................................10

Continuous Water Temperature and Streamflow.................................................................10

Polar Organic Compound Integrative Samplers...................................................................11

Focused Studies..................................................................................................................................11

Sampling Pesticides With Small-Volume Pesticide Automated Samplers ......................12

Sampling Suspended Sediment With Walling Tube Samplers...........................................12

Assessing Algal Productivity ...................................................................................................12

Ecological Surveys .............................................................................................................................13

Aquatic Biota..............................................................................................................................13

Fish Mercury Samples ..............................................................................................................14

Sediment Samples.....................................................................................................................15

Physical Habitat .........................................................................................................................15

Sample Analyses..........................................................................................................................................16

Continuous Water Temperature and Streamflow..........................................................................16

Chemical Analyses of Water, Sediment, and Fish.........................................................................16

Discrete Water-Quality Samples.............................................................................................16

Pesticides From the Small-Volume Pesticide Automated Samplers.................................17

Polar Organic Compound Integrative Samplers...................................................................17

Sediment Samples.....................................................................................................................17

Periphyton Samples for Assessing Algal Productivity ........................................................18

Ecological Surveys .............................................................................................................................18

Aquatic Biota..............................................................................................................................18

Sediment Toxicity Testing.........................................................................................................19

Physical Habitat .........................................................................................................................19

Quality Assurance and Quality Control ....................................................................................................19

Water-Quality Data-Management Procedures.......................................................................................21

Atlantic Highlands Flow-Ecology Study...................................................................................................23

Summary........................................................................................................................................................26

References Cited..........................................................................................................................................26

Appendix 1. Description of the Sampling Timelines, Matrix, Collection, and Processing

for Water, Sediment, and Ecological Samples ..........................................................................43

Appendix 2. Description of the U.S. Geological Survey National Water Quality Laboratory

Schedules Used for Water, Sediment, and Periphyton............................................................44
iv

Figures

1. Map showing locations of the Regional Stream Quality Assessment studies across

the United States ..........................................................................................................................3

2. Maps showing the Northeast Stream Quality Assessment (NESQA) study area..............4

3. Ternary diagram showing the relative percentages of undeveloped (mostly

forested), urban, and agricultural land cover in watersheds of the 95 streams

investigated for the Northeast Stream Quality Assessment (NESQA) in 2016 ...................8

Tables

1. Characteristics of stream watersheds in the northeastern United States that were

assessed as part of the U.S. Geological Survey Northeast Stream Quality

Assessment in 2016 ....................................................................................................................34

2. Summary of data collected at each of the Northeast Stream Quality Assessment

sites in 2016..................................................................................................................................38

3. Timeline of the sample collection by site type for the U.S. Geological Survey

Northeast Stream Quality Assessment in 2016........................................................................9

4. Summary counts of environmental, field blank, replicate, and spike samples of

stream water from the 95 stream sites sampled in the Northeast Stream Quality

Assessment of the U.S. Geological Survey National Water-Quality Assessment

Project in 2016. ...........................................................................................................................20

5. Stream watersheds that were included in the Atlantic Highlands flow-ecology

study, conducted by the U.S. Geological Survey as part of the National

Water-Quality Assessment Project in 2014 ............................................................................24
v

Conversion Factors

International System of Units to U.S. customary units

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

micrometer (μm) 3.937×10−5 inch (in.)

nanometer (nm) 3.937×10−8 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

meter (m) 1.094 yard (yd) 

Area

square meter (m2) 0.0002471 acre 

square meter (m2) 10.76 square foot (ft2) 

square centimeter (cm2) 0.1550 square inch (ft2) 

square kilometer (km2) 0.3861 square mile (mi2)

Volume

microliter (μL) 2.642×10−7 gallon (gal)

milliliter (mL) 0.0002642 gallon (gal)

liter (L) 0.2642 gallon (gal)

liter (L) 61.02 cubic inch (in3) 

microliter (μL) 6.102×10−5 cubic inch (in3)

Flow rate

meter per second (m/s) 3.281 foot per second (ft/s) 

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

nanogram (ng) 3.527×10−11 ounce, avoirdupois (oz)

gram per square meter (g/m2) 0.0002048 pound per square foot (lb/ft2)

milligram per square meter (mg/m2) 3.277×10−6 ounce, avoirdupois, per square foot (oz/ft2)

Pressure

kilopascal (kPa) 0.1450 pound-force per inch (lbf/in [or psi])

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as

 °F = (1.8 × °C) + 32. 

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as

 °C = (°F – 32) / 1.8. 

Datum

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

Supplemental Information

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 

25 °C).

Concentrations of chemical constituents in water are given either in milligrams per liter 

(mg/L), micrograms per liter (μg/L), or nanograms per liter (ng/L). Concentrations of chemical 

constituents in bed sediment are given in micrograms per kilogram (μg/kg).

Abbreviations

ASE accelerated solvent extraction

ASR analytical service request

CEC Commission for Environmental Cooperation

CERC Columbia Environmental Research Center

DAI direct aqueous injection

DOC dissolved organic carbon

ELISA enzyme-linked immunosorbent assay

EPA U.S. Environmental Protection Agency

ESI electrospray ionization

GC/MS gas chromatography mass spectrometry

GC–MS/MS gas chromatography-tandem mass spectrometry

GIS geographic information system

INSTAAR Institute of Arctic and Alpine Research

LC–MS/MS liquid chromatography tandem mass spectrometry

MRM multiple reaction monitoring

NAWQA National Water-Quality Assessment Project

NESQA Northeast Stream Quality Assessment

NHDPlus National Hydrography Dataset Plus

NLCD National Land Cover Database

NWIS National Water Information System

NWQL National Water Quality Laboratory

NYWSC New York Water Science Center

OGRL Kansas Organic Geochemistry Research Laboratory

OPP Office of Pesticide Programs

OTU operational taxonomic unit

PAH polycyclic aromatic hydrocarbon

PAR photosynthetically active radiation
vii

PBDE polybrominated diphenyl ether

PCB polychlorinated biphenyl

PCFF Personal Computer Field Form

POCIS polar organic chemical integrative sampler

PVC polyvinyl chloride

QA quality assurance

QC quality control

QW quality of water

QWDATA Water-Quality System within NWIS

QWDX Water Quality Data Exchange

RP reference point

RSQA Regional Stream Quality Assessment

RTH richest targeted habitat

TERL Trace Elements Research Laboratory

THg total mercury

USGS U.S. Geological Survey

UVA ultraviolet absorbance

WSC Water Science Center

Design and Methods of the U.S. Geological Survey 

Northeast Stream Quality Assessment (NESQA), 2016

By James F. Coles, Karen Riva-Murray, Peter C. Van Metre, Daniel T. Button, Amanda H. Bell, Sharon L. Qi, 

Celeste A. Journey, and Richard W. Sheibley

Abstract

During 2016, as part of the National Water-Quality 

Assessment Project (NAWQA), the U.S. Geological Survey 

conducted the Northeast Stream Quality Assessment (NESQA) 

to investigate stream quality in the northeastern United States. 

The goal of the NESQA was to assess the health of wadeable 

streams in the region by characterizing multiple water-quality 

factors that are stressors to aquatic life and by evaluating the 

relation between these stressors and the condition of biological communities. Urbanization, agriculture, and human 

modifications to streamflow are anthropogenic changes that 

greatly affect water quality in the region; consequently, the 

study design primarily selected sites and targeted stressors 

associated with these activities. The NESQA built on a prior 

NAWQA study conducted in the region in 2014, the Atlantic 

Highlands flow-ecology study, which investigated the effects 

of anthropogenically modified flows on aquatic biological 

communities in primarily forested watersheds. Land-cover 

data for the NESQA were used to identify and select sites 

within the region that had watersheds ranging in levels of 

urban and agricultural development. A total of 95 sites were 

selected: 67 on streams in watersheds representing a range of 

urban land use, 13 on streams in watersheds with some degree 

of agricultural land use, and 15 on streams in predominantly 

forested watersheds with little development. Depending on 

land-cover characteristics, sites were sampled weekly for 

metal and organic contaminants, nutrients, and sediment for 

either a 9-week period that began the week of June 6, 2016, or 

a 4-week period that begin the week of July 11, 2016. Beginning August 1, 2016, and for about 2 weeks, an ecological 

survey was conducted at every site to assess stream habitat, 

and algal, benthic invertebrate, and fish communities. Additional samples collected during the ecological surveys were 

streambed sediment for chemical analysis and toxicity testing, 

and fish tissue for mercury analysis. This report describes 

the various study components and methods of the NESQA 

and describes a precursor effort for the Atlantic Highlands 

flow-ecology study. Details are presented for measurements 

of water quality, sediment chemistry, streamflow, and ecological surveys of stream biota and habitat, as well as processes 

of sample analysis, quality assurance and quality control, and 

data management.

Introduction

Many natural and anthropogenic stressors can affect 

stream ecosystems, and often the stressors that degrade 

streams are associated with the predominant land use in a 

region. Variations in streamflow, habitat, temperature, and 

levels of sediment and nutrients are essential characteristics 

of natural stream ecosystems, but deviation from the natural 

patterns of streams can substantially alter their biological 

condition and ecological function (Lenat and Crawford, 1994; 

Gregory and Calhoun, 2006; Nagy and others, 2011). Contaminants differ from other stressors in that most are derived 

from human activities and, through various modes of action 

and toxicity, are potentially detrimental to aquatic life as well 

as to humans who use water resources. In order to efficiently 

manage water resources, it is important to understand the 

conditions under which stressors—individually or in combinations—adversely affect the biological condition of streams and 

the water resources valued by people.

Multistressor effects are often assessed in the laboratory 

under controlled conditions or in the field at small-catchment 

scales. At these small scales, biogeochemical processes and 

complex environmental interactions can be manipulated and 

monitored; however, results of such studies are not readily 

extended over larger spatial scales. Alternatively, by characterizing the conditions of multiple streams over a broad 

spatial area, specific stressors and biological conditions can be 

evaluated on regional and national scales (U.S. Environmental 

Protection Agency, 2006; Herlihy and others, 2008); from such 

studies, empirical models have been developed to predict metrics of biological condition and environmental stressors across 

national-scale disturbance gradients (Waite and others, 2000; 

Klemm and others, 2003; Herlihy and others, 2006; Coles and 

others, 2012). To date, however, most regional- and nationalscale studies have not included a thorough characterization 

of stressors but have limited their evaluations to relations 

between land use and biological condition.

The U.S. Geological Survey (USGS), through the 

National Water-Quality Assessment Project (NAWQA), is conducting studies to bridge this gap, through extensive stressor 

characterizations at large spatial scales that include multiple 

sampling sites to promote development of empirical models. 

As such, the studies are intended to provide communities and 
2 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

policymakers with information about the human and environmental factors that have the greatest effects on stream quality 

by addressing these objectives:

1. Determine the status of stream quality across the region 

on the basis of contaminants, nutrients, sediments, 

toxicity of the bed sediments, streamflow, habitat, and 

biological communities.

2. Evaluate the relative influence of contaminants, nutrients, sediment, toxicity, streamflow, and habitat on 

biological communities in the streams.

3. Evaluate how the natural and anthropogenic characteristics of the watersheds are related to stressors measured at 

the stream-reach scale and how the condition of biological communities can be explained by these stressors.

4. Develop statistical models and management tools to predict the ecological health of wadeable streams throughout the region and how it is associated with concentrations of contaminants, nutrients, and sediment.

Background

The USGS launched Cycle III of the NAWQA in 2013, 

which marked the beginning of NAWQA’s third decade of 

water-quality assessments for the Nation. In 1992, Cycle I of 

NAWQA began investigations with an emphasis on characterizing the Nation’s streams and aquifers through a routine 

monitoring program to establish baseline conditions. A decade 

later, NAWQA transitioned to Cycle II, which emphasized 

trends and modeling and included five “topical” studies 

designed to improve our understanding of environmental processes. The topical studies addressed (1) the fate and transport 

of agricultural chemicals, (2) effects of urbanization on stream 

ecosystems, (3) effects of nutrient enrichment on stream ecosystems, (4) transport of contaminants to public-supply wells, 

and (5) bioaccumulation of mercury in stream ecosystems. 

Cycle III is built on 20 years of NAWQA studies that describe 

linkages between contaminant sources and their transport to 

receiving waters and the effects of land use on stream quality 

and ecological condition.

Among the major objectives in Cycle III is to assess the 

occurrence and effects of multiple instream stressors on stream 

quality. Termed Regional Stream Quality Assessment (RSQA) 

studies, these studies are characterizing watershed and stream 

water-quality stressors and aquatic biological conditions to 

improve understanding of stressor-effects relations at regional 

scales (https://webapps.usgs.gov/RSQA/). Each RSQA 

study is a short-term assessment of wadeable streams within 

a targeted, multistate region, generally delineated by U.S. 

Environmental Protection Agency (EPA) ecoregions (Omernik 

and Griffith, 2014). About 100 streams are sampled in each 

RSQA study to investigate stream ecology and the influences 

of multiple physical and chemical stressors that are primarily 

associated with urban development and agricultural land use. 

Wadeable streams are selected across gradients in urban or 

agricultural land use or both, depending on the dominant land 

uses in the region. Weekly water sampling was conducted for 

4 to 12 weeks (depending on region and site) for a wide range 

of chemical constituents, as well as continuous monitoring of 

flow or stage and temperature in the streams. The timing of 

this water-quality “index period” is designed to capture the 

spring and early summer growing season when pesticide and 

fertilizer applications are highest. The water-quality index 

period culminates with collection of streambed sediment for 

extensive chemical analyses and toxicity testing, and with an 

ecological survey to assess stream habitat and algal, invertebrate, and fish communities.

In 2016, an RSQA study was conducted as part of the 

NAWQA to assess stream quality across the Northeast region 

of the United States. Designated as the Northeast Stream 

Quality Assessment (NESQA), this study was the fourth of 

the five NAWQA Cycle III regional studies (fig. 1); others 

were the Midwest Stream Quality Assessment in 2013 (U.S. 

Geological Survey, 2012), the Southeast Stream Quality 

Assessment in 2014 (Van Metre and Journey, 2014), the 

Pacific Northwest Stream Quality Assessment in 2015 (Van 

Metre, and others, 2015), and the California Stream Quality 

Assessment in 2017 (Van Metre, Egler, and May, 2017). The 

study area for the NESQA included 95 watersheds in 8 States: 

Connecticut, Massachusetts, New Hampshire, New Jersey, 

New York, Pennsylvania, Rhode Island, and Vermont (fig. 2A; 

table 1, in back of report). Like the preceding RSQA studies, 

the 2016 NESQA primarily investigated stressors associated 

with urban development, which is particularly intense along 

the corridor from Boston, Massachusetts, to New York City, 

New York, and agriculture, which is concentrated mainly in 

watersheds across the southwestern area of the NESQA region 

(New York and Pennsylvania).

A related NAWQA study, on which the 2016 NESQA 

study was built, was the Atlantic Highlands flow-ecology 

study conducted in 2014 at 66 sites in the Atlantic Highlands 

ecoregion to assess how flow alterations affected biological 

communities. The Atlantic Highlands is a Level II ecoregion 

that is based on ecoregion designations by the Commission 

for Environmental Cooperation (CEC) in North America 

(Omernik and Griffith, 2014), and it closely corresponds to the 

EPA Level III Northeastern Highlands ecoregion. The Atlantic 

Highlands (and thus Northeastern Highlands) includes the 

higher elevation sections in the NESQA study area, mainly 

across the more northern latitudes (fig. 2B); this area is 

generally less developed and more heavily forested than 

other ecoregions in the Northeast, and it has many streams 

whose flow has been anthropogenically altered to create water 

supplies, hydropower, recreational areas, and flood controls. 

Consequently, the Atlantic Highlands flow-ecology study was 

conducted to assess how biological communities were affected 

specifically by stressors associated with altered streamflows in 

otherwise low-disturbance streams. To help provide a context 

with the 2016 NESQA study, an overview of the Atlantic 

Highlands flow-ecology study is provided in a separate section 

near the end of this report.
Introduction 3

130° 120° 110° 100° 90° 80° 70°

45°

40°

35°

30°

25°

PACIFIC

OCEAN

ATLANTIC

OCEAN

CANADA

MEXICO

Base map image is the intellectual property of Esri and is used herein under license.

Copyright © 2014 Esri and its licensors. All rights reserved.

Base modified from Esri digital data, 1:70,000 (Esri, 2009)

Base map of states from U.S. Geological Survey 1:2,000,000 digital data

Albers Equal-Area Conic projection, standard parallels 29°30'

and 45°30', central meridian 96°, latitude of origin 23°

0 250 500 MILES 125

0 250 500 KILOMETERS 125

GULF OF

MEXICO

CSQA

PNSQA

NESQA

MSQA

SESQA

EXPLANATION

Land Cover

Open water

Urban

Scrub/grass

Forest/wetlands

Pasture/hay

Cultivated crops

Land cover modified from National Land Cover Database 2011

Figure 1. Locations of the Regional Stream Quality Assessment studies across the United States. CSQA, California Stream Quality 

Assessment; MSQA, Midwest Stream Quality Assessment; NESQA, Northeast Stream Quality Assessment; PNSQA, Pacific Northwest 

Stream Quality Assessment; SESQA, Southeast Stream Quality Assessment.

Purpose and Scope

This report describes the design and methods of the 

NESQA, a study in the northeastern United States incorporating a network of 95 stream sites sampled over several weeks 

during late spring and summer of 2016 to evaluate stream 

conditions related to water quality, sediment quality, biological communities, streamflow, water temperature, and habitat 

characteristics. The methods described include the collection 

and processing of several kinds of water-quality samples and 

ancillary data, the discussion of which is divided into three 

parts: comprehensive data collected at all sites, data collected 

at selected sites as part of focused studies, and data collected 

in the ecological surveys that took place at the end of the 

study period. The report also describes methods of laboratory 

analysis and other data processing, quality assurance and quality control procedures, and data management procedures. A 

precursor study in the Northeast that was completed in 2014, 

the Atlantic Highlands flow-ecology study, is summarized near 

the end of the report.

Study Area Description

The 95 NESQA streams sampled in 2016 were initially 

selected, in part, to constrain natural variably among sites to 

the extent practicable. A map of the CEC Level II ecoregion 

designations was used for this purpose because land-cover 

delineations at this level are based on environmental characterizations assessed at a broad regional scale (Wiken and others, 

2011). As a result, the watersheds of the NESQA streams 

were in three CEC Level II ecoregions: 76 stream sites were 

in Mixed Wood Plains, 17 sites were in Atlantic Highlands, 

and 2 sites were in the northernmost part of Southeastern 

USA Plains. The NESQA sites were also categorized by EPA 

Level III ecoregions so that the streams could be defined in 

environmental terms with greater precision (table 1, in back 

of report; fig. 2B). Much of the following information that 

describes the EPA Level III ecoregions within the NESQA 

study area is summarized from Wiken and others (2011), and 

further details are in that publication.

The Northeastern Coastal Zone had 52 NESQA sites, 

generally defines the eastern and southern boundaries of the 
4 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

MAINE

NEW YORK

PENNSYLVANIA

VERMONT

MARYLAND

MASSACHUSETTS

CONNECTICUT

NEW

HAMPSHIRE

RHODE ISLAND

NEW

JERSEY

78° 76° 74° 72° 70°

48°

46°

44°

42°

40°

Land cover modified from National Land Cover Database 2011

ATLANTIC

OCEAN

Base map image is the intellectual property of Esri and is used herein

under license. Copyright © 2014 Esri and its licensors. All rights

reserved. Base modified from Esri digital data, 1:70,000 (Esri, 2009)

Web Mercator Projection World Geodetic System of 1984 (WGS 84)

CANADA

0 50 100 MILES

0 50 100 KILOMETERS

Land cover

Water

Urban

Grasslands and other

Forest/wetlands

Pasture/hay

Cultivated crops

Agricultural

Forested

Light urban

Urban

Atlantic Highlands

flow-ecology study

(2014)

NESQA site type (2016)

EXPLANATION

A

Figure 2. The Northeast Stream Quality Assessment (NESQA) study area. A, sampling locations and generalized land 

cover. B, U.S. Environmental Protection Agency (EPA) Level III ecoregions. In 2016, 95 streams in urban, agricultural, and 

forested settings were sampled. As part of the Atlantic Highlands flow-ecology study in 2014, 66 streams in forested settings 

were sampled; 6 of these streams were also part of the NESQA site network, which are indicated by a green diamond with a 

blue dot. Site types are defined in table 1, footnote 3.
Introduction 5

MAINE

NEW YORK

PENNSYLVANIA

VERMONT

MARYLAND

MASSACHUSETTS

CONNECTICUT

NEW

HAMPSHIRE

RHODE ISLAND

NEW

JERSEY

78° 76° 74° 72° 70°

48°

46°

44°

42°

40°

ATLANTIC

OCEAN

Basemap image is the intellectual property of Esri and is

used herein under license. Copyright © 2014 Esri and

its licensors. All rights reserved. Base modified from Esri

digital data, 1:70,000 (Esri, 2009)

CANADA

EXPLANATION

Eastern Great Lakes Lowlands

Northeastern Coastal Zone

Northeastern Highlands

Northern Allegheny Plateau

Level III ecoregion (EPA)

Northern Piedmont

0 50 100 MILES

0 50 100 KILOMETERS

Boston

Albany

Rochester Syracuse Buffalo

Hartford

Providence

B

Figure 2. The Northeast Stream Quality Assessment (NESQA) study area. A, sampling locations and generalized land 

cover. B, U.S. Environmental Protection Agency (EPA) Level III ecoregions. In 2016, 95 streams in urban, agricultural, and 

forested settings were sampled. As part of the Atlantic Highlands flow-ecology study in 2014, 66 streams in forested settings 

were sampled; 6 of these streams were also part of the NESQA site network, which are indicated by a green diamond with a 

blue dot. Site types are defined in table 1, footnote 3.—Continued
6 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

NESQA region, and encompasses the urban corridor of Boston, Mass., Providence, Rhode Island, Hartford, Connecticut, 

and New York City, N.Y. This ecoregion has much greater 

concentrations of human population than does the westerly 

adjacent ecoregion, the Northeastern Highlands. Attempts 

were made to farm much of the Northeastern Coastal Zone 

after the region was settled by Europeans, but land use now 

mainly consists of urban and suburban development, regrowth 

forests and woodlands, and only small areas of pasture 

and cropland.

The Eastern Great Lakes Lowlands had 14 NESQA sites 

and extends over the lowlands centered on the lower reaches 

of the St. Lawrence and Hudson Rivers. This ecoregion, being 

characterized by lowlands, surrounds sections of the Northeastern Highlands ecoregion in New York and defines the 

western boundary of the NESQA region. Although some urban 

centers are in this ecoregion, such as Syracuse, Rochester, 

and Buffalo, N.Y., 60 percent of the ecoregion is intensively 

cultivated farmland with the dominant farming systems being 

mixed, dairy, and cash crops. Major crops include grains, corn, 

soybeans, hay, and fruits and vegetables; orchards and vineyards are also important for the region.

The Northern Allegheny Plateau had 14 NESQA sites, 

defined the southwest boundary of the NESQA region, and 

included parts of southern New York and northern Pennsylvania. The terrain is glaciated upland plateau, which contains 

rolling hills, open valleys, and low mountains, and the geology 

is mostly shales, siltstones, and sandstones. Urban development is relatively low in this ecoregion, although it does have 

multiple towns and small cities. Much of this ecoregion can be 

characterized generally as a mosaic landscape that has farms 

interspersed with areas of woodlands and forest. The principal crops of the farms are pasture, hay, and grain for beef and 

dairy cattle.

The Northeastern Highlands had 13 NESQA sites, 6 of 

which were also sampled for the 2014 Atlantic Highlands 

flow-ecology study. This Level III ecoregion covers most of 

the northern and mountainous parts of New England, as well 

as the Adirondack and Catskill Mountains in New York State. 

More forest-covered than the adjacent ecoregions, it has considerable variety in its tree species and has many moderateto-high-gradient perennial streams. A primary reason sites 

were chosen in this ecoregion is that it has many streams with 

forest-dominated watersheds that are minimally disturbed by 

human land use. The streams in this ecoregion that were used 

in the Atlantic Highlands flow-ecology study collectively 

represented a gradient of low to high levels of flow alteration. 

However, the 2016 NESQA sites in this ecoregion were at the 

low end of the flow-alteration gradient and, therefore, were 

among the least disturbed sites in the NESQA study.

Two NESQA sites in New Jersey were in the Northern 

Piedmont. This ecoregion extends as far north as northern 

New Jersey and extends through that State as a narrow band 

bordered on the west by the Northern Appalachian Plateau 

ecoregion and on the east by the Atlantic Maritime Highlands 

and the Northeastern Coastal Zone ecoregions; thus, the 

Northern Piedmont generally is situated between mountain 

ranges and the coastal plain. The climate in this area of the 

Northern Piedmont generally is marked by hot summers 

and cold winters, it has low to moderate gradient perennial 

streams, and topography can be characterized as having low, 

rounded hills. Pre-Columbian vegetation was predominately 

Appalachian oak forests but now includes chestnut oak, white 

oak, red oak, hickories, ash, elm, and yellow-poplar; eastern 

red cedar is common on abandoned farmland. Mostly agriculture and urban, suburban, and industrial uses prevail, but in the 

vicinity of the NESQA sites, land cover is primarily developed, including urban and suburban land uses.

Study Design

The NESQA study was designed to assess differences 

in stream quality that were associated with urban development and agriculture in the region and to identify and measure 

specific stressors linked to those land uses. The NESQA study 

expanded on the 2014 Atlantic Highlands flow-ecology study 

that assessed changes in the quality of Northeast streams relative to the type and extent of flow-regime modifications.

Of the 95 NESQA stream sites that were sampled during 

2016, 63 were primarily selected to characterize the effects of 

urban development and associated stressors on stream health, 

and 17 were selected to characterize the effects of agriculture and associated stressors on stream health; additionally, 

15 sites were predominantly forested, with less than 1 percent 

of urban and less than 5 percent agricultural land use in their 

watersheds, and these sites were used to help establish “least 

developed” conditions for most stressors examined here. The 

network of 67 urban-development sites represented a gradient 

design, in which the watersheds represented a range of urban 

development from near zero to 99 percent. The 13 agricultural 

sites were incorporated in a group design, which grouped 

sites in 1 of 3 categories based on the relative percentage of 

agricultural land use in the watershed (1 to 5, greater than 5 to 

15, and greater than 15 percent). The forested sites were used 

in conjunction with both the urban and agricultural sites, either 

to characterize the least developed end of the urban gradient or 

near-reference conditions for the agricultural gradient.

Site Selection

Only wadeable streams were considered for the study 

because they generally had a depth of about 1 m or less during 

low flow, which is shallow enough to be sampled by wading. 

In selecting streams for the NESQA study, candidate sites 

were identified first from active and historical (inactive) USGS 

streamgages, then from other USGS sampling sites and from 

monitoring sites used by State and local agencies. Several sites 

that had not been previously sampled were also selected to fill 

gaps in the distribution of land-use settings relative to design 

objectives. A geospatial database was created that included 
Sample Collection and Processing 7

land-cover characteristics for the watersheds of all candidate 

sites. Watershed delineations and characteristics were available 

for active USGS streamgages; however, for other candidate 

sites, catchment boundaries from the National Hydrography 

Dataset Plus were used as the watershed boundaries by 

selecting all upstream catchments from the segment on which 

the candidate site was located (NHDPlus Version 2; U.S. 

Environmental Protection Agency, 2012). Nationally available, 

digital geographic information systems (GIS) data layers (for 

example, the National Land Cover Database [NLCD], Homer 

and others, 2015) were overlain on the catchment-derived 

watersheds, and then characteristics of the watersheds were 

assessed and summarized from these data layers.

Initially, 630 sites were identified in the NESQA region. 

These were subsequently evaluated with the use of Google 

Earth satellite imagery (https://www.google.com/earth/) for 

general watershed characteristics related to land cover and 

geomorphology, potential stressor sources (for example, 

water treatment plants, industrial complexes, golf courses), 

and sampling reach locations. From this procedure, 178 sites 

were selected as potential sampling streams that collectively 

represented forest, agricultural, and urban development land 

uses. An instream reconnaissance of these sites was conducted 

by USGS staff during the summer of 2015; field observations 

for each site included evaluating the site for access and safety, 

assessing general stream characteristics to determine a watersampling location, and identifying a 150-meter (m) stream 

reach with riffle habitat suitable for conducting ecological 

surveys. Information that was documented included stream 

accessibility, location and description of the nearest bridge 

for water-chemistry sampling during high flows, stream-reach 

wadeability, streambed substrate, instream habitat complexity, 

presence of discharge pipes and other obvious point sources, 

potential landowner contacts, and photographs of the stream. 

Field notes and photography were recorded onsite by using 

field-reconnaissance forms on an electronic tablet; afterwards, 

information from these forms was compiled into spreadsheets 

for use in site review for final selection.

Land-Use Designations

The designations of the three types of NESQA sites—

urban development, agricultural, and forested undeveloped—

were based on percentages of land cover in their watersheds 

(fig. 3). Candidate urban-development sites were selected 

on the basis of the percentage of urban land use and lack of 

substantial (about 5 percent or less) agricultural row-crop 

land use from the 2011 NLCD data (U.S. Geological Survey, 

2014; Homer and others, 2015). To ensure that the network of 

urban-development sites characterized a gradient of urbanization from low to high levels, sites were selected to fit within 

one of five categorical “tiers” that each represented a different range of watershed urban land cover: tier 1, 1–10 percent 

(considered “light urban”); tier 2, greater than 10–20 percent, tier 3, greater than 20–37.5 percent; tier 4, greater than 

37.5–50 percent; and tier 5, greater than 50 percent (table 1, in 

back of report). The 67 sites selected for the urban-development gradient were distributed across the 5 tiers so that incremental levels of urban development were represented. Urban 

development in the region is concentrated along the southern 

corridor of the NESQA region that included the metropolitan 

areas of Boston, Mass., Providence, R.I., Hartford, Conn., and 

New York City, N.Y. (fig. 2B), but urban centers located elsewhere in the region were also included (for example, Albany, 

Syracuse, and Rochester, N.Y.). In addition, the predominantly 

forested sites along this section of the NESQA region were 

used in the urban-development gradient to represent least 

developed conditions.

Agricultural sites were selected to represent the major 

crop-producing areas in the western NESQA region (fig. 2A), 

and priority was given to sites in watersheds where agricultural chemical use was expected to be high on the basis of the 

crop type grown. Unlike the gradient design used to characterize increasing levels of urban development among sites, the 

agricultural network of 13 sites included 2 categories that each 

represented a range of land-use percentages in cultivated row 

crops: low Ag, 5 to 15 percent agriculture, and Ag, greater 

than 15 percent agriculture (table 1, in back of report). In addition, 4 of the 15 “Forested” sites had very low agriculture, 1 to 

5 percent, and these supplemented the agricultural site groups 

(forming a third agricultural group). The balance of land use 

in the watersheds of most of these sites with very low agriculture was primarily forest with very little urban development. 

Additionally, the remaining 11 of the 15 NESQA forested 

sites helped to characterize least disturbed stream conditions 

for comparison with conditions of the agricultural sites and to 

help approximate predevelopment conditions along the urban 

gradient (fig. 3). It is important to note that the categorical 

designations used for selecting the sites were based on cursory 

reviews of watershed features and that more rigorous GIS 

procedures were used later to more accurately characterize and 

define the sites.

Sample Collection and Processing

To allocate resources effectively among the 95 NESQA 

sites, the frequency of water-quality sampling varied by the 

intensity of development in the watershed. The predominately 

forested sites were sampled weekly during the 4-week period 

that began on July 11, 2016. All 45 urban sites and 6 of the 

22 light urban sites were sampled weekly for the 9-week 

period that began on June 6, 2016; 16 of light urban sites that 

were sampled only during the 4-week period. Of the 13 agricultural sites, the 8 representing the highest level (greater than 

15 percent row crop) were sampled weekly over the 9-week 

period, whereas the sites representing the low levels (5 sites) 

of agriculture were sampled weekly only during the 4-week 

period. Further information about the sampling frequency at 

each site is provided in tables 2 (in back of report) and 3.
8 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

Urban

Undeveloped Agricultural

Figure 3. The relative percentages of undeveloped (mostly forested), urban, and agricultural land 

cover in watersheds of the 95 streams investigated for the Northeast Stream Quality Assessment 

(NESQA) in 2016. Each of the three points of the diagram represents 100 percent of the respective 

land-cover type. If a site had equal amounts of urban, agriculture, and undeveloped land cover, it 

would be centered in the diagram. Colors are for visual effect.

The types of data and the intervals at which samples were 

collected varied among the NESQA sites according to landcover type and associated potential stressors. Data collection 

routines were categorized nominally by three study-design 

components (table 2, in back of report). The comprehensive 

stream water data component began the week of June 6, 2016 

(at 59 sites), or the week of July 11, 2016 (at 36 sites), and 

continued through the week of August 8, 2016. During the 

sampling period, water temperature and streamflow were 

recorded at all sites (by data-logging instrumentation, typically on a 1-hour interval), and water-quality samples were 

collected weekly. The focused studies component included 

several investigations at subsets of NESQA streams that were 

focused on the occurrence and timing of specific stressors that 

could affect the condition of those streams; these studies are 

described below. The ecological survey component occurred 

within a 2-week period that began August 1, 2016: at each 

stream along a 150-m sampling reach during, assessments 

were made of the physical habitat and biological communities, 

and samples were collected for chemical analysis of sediment 

and mercury contamination in fish.

In addition to being characterized by study-design component, data were defined by the time interval at which they 

were collected: discrete, integrated, or continuous, depending 

on the parameter being measured (table 2, in back of report). 

Discrete data characterized conditions at a given date and 

time and could be collected once, as represented by streambed 

sediment samples collected during the ecological survey, or 

at discrete intervals, as represented by water-quality samples 

collected weekly. Integrated data represented “average” conditions over the time period the sampler was deployed, as was 

the case with the polar organic chemical integrative sampler 

(POCIS), described in the section “Polar Organic Compound 

Integrative Samplers.” Continuous data were water-quality 

parameters recorded at short but regular time intervals 

throughout a sampling period, as was the case with stream 

temperature, which was recorded hourly.

USGS staff who participated in the NESQA study 

received intensive training prior to any data collection activities, including instructions specific to water-quality sampling, 

the focused studies, and ecological surveys. For example, the 

use of low-level analytical methods necessitated that water 

samples be collected according to “parts-per-billion” protocols (U.S. Geological Survey, 2006). During weeks when 

water-quality data were collected at all 95 sites, as many as 

10 two-person teams of USGS staff were deployed. Thus, to 

ensure consistency among the water-quality teams, training 

for the collection and processing of water-quality samples 

occurred in May 2016 for all personnel involved with sample 

collection. Classroom water-quality training was followed 

by field-training exercises to work through all sampling and 

processing procedures in the field prior to the start of sampling. The sample collection timelines (table 3), sample types 

collected at sites, and sample collection, processing, and handling procedures are summarized in appendix 1 and described 

briefly here.
Sample Collection and Processing 

9

Table 3. Timeline of the sample collection by site type for the U.S. Geological Survey Northeast Stream Quality Assessment in 2016.[Timing is shown only for sampling that took place at all sites, not for components of the focused studies. %, percent; POCIS, polar organic chemical integrative sampler]

Site type Sampling type

Week of

June 6 June 13 June 20 June 27 July 4 July 11 July 18 July 25 August 1 August 8

9-week sites

Urban: All 45 Tier 2–5 sites, 6 of 22 Tier 

1 sites

Agriculture: All 8 sites with greater than 

15% row crop

Water chemistry, sampled weekly Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9POCIS Deployed RetrievedAquatic biotaPhysical habitat Ecological surveys Mercury in fish tissueSediment contaminants

4-week sites

Forested: All 15 sitesUrban: 16 of the 22 Tier 1 sitesAgriculture: All 5 sites with less than 15% 

row crop

Water chemistry, sampled weekly Week 6 Week 7 Week 8 Week 9POCIS Deployed RetrievedAquatic biotaPhysical habitat Ecological surveys Mercury in fish tissueSediment contaminants
10 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

Comprehensive Stream Water Data

To help characterize stream conditions in a consistent 

manner among NESQA sites, a comprehensive suite of 

samples and ancillary data were collected at each location over 

several weeks during the course of the NESQA study. Discrete water-quality samples were collected for a 9-week QW 

(quality of water) sampling period at 59 sites and a 4-week 

QW sampling period at 36 sites (tables 2, in back of report, 

and 3 and appendix 1, table 1.1). Continuous readings of water 

temperature and streamflow were collected at all sites for up 

to a year (including the QW and ecological sampling periods). Discharge was recorded at sites that had active USGS 

streamgages, and pressure transducers were installed to record 

stream stage during the QW and ecological sampling periods 

(or longer) at sites without active streamgages (table 2, in 

back of report). Polar organic chemical integrative samplers 

(POCISs) were deployed at all sites for about 6 weeks during 

the QW sampling period; the POCISs provided estimates of 

the average concentrations of certain organic chemicals over 

the deployment period. These samples and how they were collected are described in more detail in the following sections.

Discrete Water-Quality Samples

Weekly discrete water-quality samples were collected 

according to the following basic laboratory schedules: 

nutrients, major ions, dissolved organic carbon, pesticides, 

glyphosate by immunoassay, and suspended-sediment concentration. This group of schedules is referred to as BASIC for 

the weekly sampling routines, whereas additional chemical 

parameter groups were sampled on selected weeks (appendix 1, table 1.1). The parameter groups included in a sampling 

event and frequency of sample collection varied by site type 

so that potential stressors could be associated with land-use 

characteristics, such as timing of pesticide applications. 

Samples were collected and processed by following standard USGS protocols described in the National Field Manual 

(Wilde and others, 2009). Prior to collecting samples from 

the field, all field equipment was cleaned according to USGS 

protocols and was rinsed with native water immediately before 

samples were collected. In general, discrete water samples 

were collected for most analytes by an isokinetic, equal-width 

increment method (U.S. Geological Survey, 2006), where 

subsamples were collected at 10 increments across the stream 

with either a DH–81 or DH–95 sampler (Davis, 2005). The 

sampler had a precleaned Teflon cap and nozzle assembly 

that fitted a 1-liter (L) Teflon bottle (U.S. Geological Survey, 

2006). Each incremental sample was placed immediately 

into a precleaned, acid- and methanol-rinsed Teflon churn for 

compositing prior to processing. When stream conditions did 

not meet the requirements for collection of a representative 

equal-width increment sample (velocity greater than 1.5 foot 

per second [ft/s]), samples were collected either by a multivertical grab (velocity less than 1.5 ft/s, width greater than 

10 feet), or by a grab from the centroid of flow (velocity less 

than 1.5 ft/s, width less than 10 feet, depth less than 1 foot). 

Water was collected directly into sample bottles for unfiltered 

constituents and into a precleaned 1-L Teflon sample bottle for 

filtered constituents; samples were subsequently filtered from 

that bottle into sample bottles (appendix 1, table 1.3).

Much of the Northeast experienced a drought during the 

summer of 2016, with little or no rain for much of the QW 

sampling period; as a result, many streams were sampled by 

collecting grab samples near the end of the QW sampling 

period when streamflows were particularly low. In addition, 

however, dissolved organic carbon (DOC) samples were collected by a center grab regardless of flow conditions.

Field properties of specific conductance, pH, dissolved 

oxygen, and water temperature were measured at the time of 

sampling with a field-calibrated multiparameter sonde (Wilde, 

variously dated). The measurements were made at five locations within the water-quality sampling transect. When the 

stream width was less than 3 m, parameters were collected 

from the centroid of flow. In addition to constituents sampled 

in all weekly visits previously noted, samples for other waterquality constituents were collected on selected weeks during 

the QW sampling periods: isotopes of nitrate (15N and 18O), 

organic wastewater indicators and pharmaceuticals, algal 

toxins, mercury (total and methyl), and ultraviolet absorbance (specific weeks when constituents were sampled are 

identified in appendix 1, table 1.1). Ultratrace-concentration 

clean-sampling procedures and equipment were used to collect 

samples for low-concentration total mercury and methylmercury analysis (U.S. Environmental Protection Agency, 1996; 

Lewis and Brigham, 2004). These were grab samples collected 

at about 0.3 m below the water surface in a Teflon bottle; five 

samples were collected at the 9-week sites, and three samples 

were collected at the 4-week sites, (table 2, in back of report; 

appendix 1, table 1.1).

Continuous Water Temperature and Streamflow

Digital temperature data loggers were used to continuously monitor water temperature at all stream sites. The 

devices recorded temperature at 1-hour intervals and were 

deployed during the early fall of 2015 and retrieved about 

a year later, in order to provide a water temperature dataset 

inclusive of all NESQA sampling activities. (Exceptions were 

several sites with USGS streamgages where continuous temperature loggers had been previously installed.) Where possible, loggers were deployed approximately 10 centimeters (cm) 

above the streambed, out of direct sunlight, and attached 

to rebar anchored into the streambed or to stable parts of 

streamgage infrastructure (for example, orifice pipe). In 

most cases, the HOBO Water Temp Pro v2 U22 loggers were 

deployed (device specifications are in appendix 1, table 1.2). 

Guidance from the manufacturer and the U.S. Forest Service 

concerning deployment, calibration, and maintenance generally was followed (Dunham and others, 2005; Onset Computer 

Corporation, 2012).
Sample Collection and Processing 11

USGS streamgages were active at 54 NESQA sites and 

provided stream stage and streamflow discharge at 15-minute 

intervals (table 2, in back of report). Water-level loggers were 

deployed at the 41 sites where streamgages did not exist; 

these loggers recorded stream stage (and water temperature) at 

hourly intervals. The NESQA study used the HOBO U20–

001–04 digital water level loggers (specifications are in appendix 1, table 1.2). In most cases, the units were deployed during 

the spring of 2016, prior to the start of the QW sampling 

periods, and remained deployed until the fall of 2016. Guidance from the manufacturer and the USGS for deployment, 

calibration, and maintenance was followed (Onset Computer 

Corporation, 2014; Sauer and Turnipseed, 2010).

Deployment included the installation of two water-level 

loggers per site: one mounted in the water column to measure 

changes in water pressure as the water level changed, and one 

mounted in the air to measure barometric pressure to provide 

a correction factor for calculating stream stage. The loggers 

were mounted inside a vertical 2-inch polyvinyl chloride 

(PVC) pipe mounted to a bridge support or directly to a metal 

post driven into the streambed. The water-pressure loggers 

were mounted at a depth where the unit would remain continually submerged, and the barometric-pressure loggers were 

typically mounted in the air at the top of the pipe or post; both 

were programmed to record on hourly intervals for the duration of the study.

Establishing a baseline water-level was necessary 

immediately after installation of the water level loggers so 

that logger readings in water pressure could be converted to 

actual water level. A reference point (RP), on which changes 

in water level were based, was established above the pool that 

held the submerged water-level logger. Typically, the RP was 

a mark scribed on a permanently fixed structure adjacent to 

the attached logger, such as a bridge support or wing wall; a 

measurement from the RP to the water surface was the “tape 

down” distance. An arbitrary datum was then established that 

was greater than the distance between the RP and the channel bottom, and this datum would cover all low stages and 

ensure no negative stage values; typically, 10 feet was used. 

The distance from the RP to the surface of the water at time 

of deployment was used to establish the initial stream stage. 

In addition, measurements from the RP to water surface were 

made during at least one of the site visits by the water-quality 

sampling crew so that these values could be used to check the 

data for consistency and quality.

Polar Organic Compound Integrative Samplers

The POCISs are designed to accumulate water-soluble 

(polar or hydrophilic) organic compounds from surface water. 

These integrative samplers were deployed at all NESQA sites 

during the week of June 20 and retrieved during the last waterquality sampling visit during the week of August 1 (tables 2, 

in back of report, and 3). Four POCISs containing the sorbent 

Oasis HLB (Waters, Milford, Mass.) (Alvarez, 2010) were 

deployed in a single canister at each of the 95 sites. Oasis 

HLB is considered a universal sorbent in environmental analyses and has been used to extract a wide assortment of chemical classes from water. The use of Oasis HLB in the POCIS 

provided a mechanism to estimate time-weighted average 

concentrations of target chemicals, pharmaceuticals, and pesticides. The POCIS extracts were analyzed for concentrations 

of pesticides and pharmaceuticals by using modified versions 

of the water methods for these chemical groups (Van Metre, 

Alvarez, and others, 2017).

Field deployment followed the guidelines provided in 

Alvarez (2010). Successful deployment required a stream 

location with sufficient depth (about 15 cm) for the sampler 

to remain submerged during the deployment period and be 

protected from excessive sediment accumulation and flood 

debris and from vandalism. Effective anchoring systems 

were adopted on the basis of site-specific characteristics (for 

example, sandy versus rocky substrate, streamflow variability, 

and so forth). The POCIS was attached coincident with the 

temperature data logger at many sites, either on the rebar or on 

the orifice pipe. Field records were maintained that included 

the site name, date and time of deployment and retrieval, and 

observations of streambed substrate, streamflow conditions, 

and water clarity.

About 10 percent of the POCISs were accompanied by 

field blanks that were used to assess any accumulation of 

target and nontarget compounds from the air during shipment 

and deployment. The POCIS field-blank protocol specified 

that the blank canisters be open to the air at the same time and 

place as the field POCISs were exposed to air during deployment and retrieval. Between deployment and retrieval of the 

field POCISs, the POCIS blank canisters were kept sealed and 

stored between −20 and 0 °C. All field POCISs and blank canisters were stored on ice during transport to and from the field 

location. After the 6-week deployment period, the POCISs 

were retrieved from the sites and immediately sealed in their 

respective canisters; the POCISs, field blanks, and log sheets 

were shipped to the USGS Columbia Environmental Research 

Center (CERC) in coolers with wet ice.

Focused Studies

Three types of focused studies were conducted at selected 

NESQA sites. Small-volume pesticide automated samplers 

were deployed at seven sites to collect daily-composited water 

samples for pesticide analysis. Walling tubes were deployed at 

14 sites to collect integrated samples of suspended sediment. 

Algal productivity was evaluated at five sites with the use of 

nitrate, dissolved oxygen, pH, and conductivity data that were 

collected continuously and chlorophyll a samples that were 

collected monthly from April through September.
12 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

Sampling Pesticides With Small-Volume 

Pesticide Automated Samplers

A small-volume pesticide autosampler (hereafter, “pesticide autosampler”) was designed and built at Portland State 

University to collect fixed-point, small-volume samples for 

analysis of pesticides in water using newly developed direct 

aqueous injection (DAI) methods. The samplers were used in 

the NESQA study to help determine if increasing sampling 

frequency would improve the accuracy of characterizations 

of instream pesticide stressor conditions to which biota were 

subjected, in particular short-duration but acutely toxic events. 

Although weekly discrete samples of pesticides were collected at all sites during the QW sampling periods (with some 

exceptions, described in a later section, “Sample Analyses”), 

discrete samples might not detect short-term “spikes” in high 

concentrations that are potentially acutely toxic. Pesticide 

autosamplers were deployed at one agricultural site and six 

urban sites (greater than 50 percent agriculture or urban, 

respectively) to collect daily and weekly composite samples 

over the 9-week QW sampling period (table 2, in back 

of report).

The pesticide autosamplers were programmed to collect 

multiple aliquots to form daily and weekly composite samples 

of stream water over successive 1-week periods. An aliquot of 

stream water was collected every 6 hours into daily-composite 

vials (four aliquots per vial, with the “day” typically starting 

around noon) and every 12 hours into the weekly composite 

vial. Thus, eight vials were filled per week for seven daily 

samples and one weekly sample. In addition, a ninth vial containing a known pesticide spike mixture in native stream water 

was included to assess the potential for compound degradation during the weekly collection period. A 6-mL aliquot of a 

1:1 methanol-water mixture was added, as a preservative, to 

each of the nine vials before deployment.

Over the 9 weeks of operation, the pesticide autosamplers 

were serviced each week on either Monday or Tuesday. Two 

units were available for each of the seven sites so that one unit 

could be serviced in the laboratory and exchanged in the field 

for the deployed unit. This arrangement minimized interruption by allowing ample time to remove and replace sample 

vials, charge batteries, clean tubing, and replace consumable 

components such as filters. Prior to deployment, each vial was 

labeled with the station identification number, vial number, 

date, and initial weight. Daily-composite samples (vials 1 

through 7) were analyzed for pesticide concentrations by the 

EPA Office of Pesticide Programs (OPP). Sample splits of 

the weekly composite sample (vial 9) and the spike sample 

(vial 8) were analyzed for pesticide concentrations by the 

USGS National Water Quality Laboratory (NWQL) in Denver, 

Colorado, and the OPP laboratory. Analytical service request 

(ASR) forms (USGS) and cooler inventory forms (USGS and 

EPA) were included with sample shipments, and barcodes 

were affixed to each vial as an auxiliary data identifier and 

tracking method.

Sampling Suspended Sediment With Walling 

Tube Samplers

Suspended-sediment samples were collected from 

14 sites by using time-integrating passive samplers, referred 

to in this report as Walling tubes (Phillips and others, 2000; 

Gellis and others, 2017). The sediments were analyzed for 

major and trace elements and radionuclides to assess sources 

and ages of sediment in the stream. The network of Wallingtube sites comprised 10 urban sites, 3 agricultural sites, and 

1 forested site (table 2, in back of report). The Walling tube 

sampler was made from commercially available PVC pipe 

(98-millimeter [mm] inner-diameter) cut to a length of approximately 1.0 m. The end facing upstream was affixed with a 

funnel that had a 4-mm stem facing outward; the downstream 

end of the tube was fitted with an endcap with a hole drilled in 

the center with a 4-mm plastic tube inserted. As water passed 

into the tube through the small opening in the funnel stem, 

the velocity decreased in the larger diameter tube, allowing 

suspended sediment to settle, and relatively clear water passed 

out of the 4-mm tube at the back. The tubes were attached to 

metal posts that were driven into the streambed and were oriented so that the funnel end faced into the flow. Typically, four 

tubes were deployed within the 150-m reach of a site, where 

two tubes were installed at each of two locations by placing 

one tube above the other on the metal posts. To ensure that 

samples consisted of suspended sediment and not bed sediment, the bottom tube was positioned at least 15 cm above the 

channel bed when it was deployed. If base flows were especially low at the time of deployment, the top tube was allowed 

to be out of water; in such cases, the top tubes would only 

collect sediment samples at higher flows.

Deployment of Walling tubes centered around late April, 

and the tubes remained deployed for approximately 20 weeks, 

through early October (inclusive of the 9-week QW sampling period); sediment was retrieved about every 4 weeks 

so that sufficient sediment could accumulate for analyses of 

major and trace elements and radionuclides. To collect the 

sediment samples, the tubes were removed from their posts, 

the end caps were opened, and the water and sediment were 

poured into a 5-gallon plastic bucket. A spray bottle filled with 

deionized water was used to rinse any remaining sediment 

from the tubes. After collecting the samples, the tubes were 

cleaned with a brush and deionized water, then rinsed with 

native water. The water-sediment mixture was stored at room 

temperature in the 5-gallon bucket until the sediment settled to 

the bottom (usually 3–7 days), then the water was siphoned off 

and discarded, and the remaining sediment was transferred to 

a sample jar and shipped on wet ice to the laboratory.

Assessing Algal Productivity

A focused investigation was conducted at five NESQA 

sites to assess nutrient dynamics at a high temporal resolution 

and to evaluate how algal productivity responds to changes in 
Sample Collection and Processing 13

water quality (table 2, in back of report). Data were collected 

as time-series measurements and included algal biomass, 

nitrate, and water-quality parameters. Three urban sites (two 

tier 1, one tier 3) and two agricultural sites were selected to 

incorporate a range of expected nutrient conditions. Sites 

were operated from April through September 2016 and were 

instrumented with an Onset photosynthetically active radiation 

(PAR) meter and YSI EXO2 and Sea-Bird SUNA continuous 

water-quality monitors, with the exception that a SUNA was 

not used to record nitrate at one site (Salmon River near East 

Hampton, Conn. [CT_SalmonHam]; although this site is categorized as tier 1 urban, the land cover is less than 4 percent 

urban, so the presumption was made that the stressor levels 

such as nitrate concentrations would be relatively low).

Continuous, discrete, and reach-level data were collected 

at the algal productivity sites. The following parameters were 

measured continuously (15-minute intervals) during the study: 

water temperature, dissolved oxygen, pH, specific conductance, turbidity, fluorescent dissolved organic matter (a proxy 

for carbon concentration), nitrate, and PAR. Discrete samples 

for nutrients, suspended sediment, and DOC were collected 

monthly at each site over the course of the study. During each 

monthly visit, data also were collected along a 90-m reach 

of the channel that encompassed 10 equally-spaced transects 

(10 m apart), established by using the methods described in 

Fitzpatrick and others (1998). Field readings for dissolved 

oxygen, specific conductance, pH, and water temperature were 

recorded at five points along a transect across the stream channel. Macrophyte coverage was estimated at 5 locations along 

each of the 10 transects, and canopy density was estimated 

with a spherical densiometer at the center of each transect. 

Periphyton samples (assumed to be dominated by benthic 

algae) were collected at the 10 transects (right, middle, or left 

portions of each transect) and were composited; subsamples 

were extracted from the composited sample and filtered onto 

0.47-μm glass-fiber filters for chlorophyll a and ash-free dry 

mass (AFDM) analysis (appendix 2.1–table 2.10) (Britton and 

Greeson, 1987; Arar and Collins, 1997).

Ecological Surveys

The data collected during the ecological surveys characterize aquatic biota, mercury in fish tissue, sediment contaminants, and physical habitat along a 150-m sampling reach of 

each site (tables 2, in back of report, and 3). Six teams, each 

consisting of six USGS employees, were deployed across the 

region to complete the sampling at all sites during August 

1–10, 2016, which was considered the shortest timeframe 

practical. The ecological surveys were timed to coincide with 

the end of the QW sampling period so that monitored waterquality conditions could be related to the biological condition. 

Some exceptions were made at a few sites, identified in table 2 

(in back of report), where certain ecological-survey components were delayed until October 2016 because of either 

very low-flow or storm events during the normal ecological 

sampling period. Although the data collected during the 

ecological surveys were based on discrete samples, biological and habitat data generally represent integrative conditions 

over some period of time. For example, sediment chemistry 

is influenced by erosional processes and contaminant persistence; the species structure of aquatic biological communities 

depends on water-quality conditions that occur over life cycles 

of the organisms; and the physical habitat of a stream reach 

is strongly affected by many years of hydrologic events and 

human actions.

To ensure consistency in collecting the biological samples 

and conducting the physical habitat surveys, most personnel 

on the sampling teams were experienced in applying the methods described in USGS ecological sampling protocols and had 

participated in previous RSQA sampling. Algal, invertebrate, 

and fish community samples were collected, and habitat was 

assessed along a 150-m ecological assessment reach at each 

stream, according to the methods described in Moulton and 

others (2002). All field data were recorded on electronic forms 

by using hand-held tablet computers. Field data collected 

from the fish and habitat surveys, and field records for the 

algal and invertebrate samples destined for laboratory analysis were loaded into the USGS BioData database, the USGS 

repository for aquatic bioassessment data (U.S. Geological 

Survey, 2016).

Aquatic Biota

Algal and invertebrate communities were sampled 

according to standard USGS richest targeted habitat (RTH) 

protocols (Porter and others, 1993; Moulton and others, 2002; 

Hambrook and Canova, 2007). RTH samples are intended 

to represent the habitat features having the greatest potential diversity of organisms within a given stream reach. All 

NESQA sites had sampling reaches with at least one riffle 

zone, the assumed RTH habitat, and algal and invertebrate 

samples were collected from these riffles.

The algal sample was collected by scraping the periphyton biofilm from rocky substrate (for example, flat cobbles) to 

obtain a targeted area of 150 cm2. The substrate was scraped 

with a brush in a defined area and flushed into a 500-mL bottle 

with native water. Typically, 11 scrapes of equal size were 

taken from rocks that were collected among the RTH riffles 

and combined into a single composited algal sample to represent the site. A total of seven aliquots were removed from the 

sample for various analyses. Four aliquots were filtered onto 

glass-fiber filters with 0.47-μm pore size for analysis at the 

NWQL of chlorophyll a and ash-free dry mass (two filters), 

and for backups in the event of sample loss or damage (two 

filters). The fifth aliquot was filtered onto a precombusted 

glass-fiber filter with 0.47-μm pore size for analysis of carbon 

and nitrogen stable isotopes (δ13C and δ15N, respectively) and 

C:N ratios at the Cornell University Stable Isotope Laboratory 

in Ithaca, N.Y. The sixth aliquot was processed in the same 

manner and served as a backup in the event of sample damage or loss, or of need for additional material for analysis. The 
14 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

seventh aliquot was put into a 2-mL vial and shipped to the 

Institute of Arctic and Alpine Research (INSTAAR) Diatom 

Laboratory at the University of Colorado Boulder for environmental DNA (eDNA) analysis. The remainder of the sample 

was preserved with buffered formalin at a concentration of 

approximately 5 percent and sent to the INSTAAR Laboratory 

for taxonomic identification and enumeration of diatoms.

A periphyton sample also was collected to ascertain if 

microcystins were present in the stream. Microcystins are a 

group of algal toxins produced during harmful algal blooms. 

The sample was collected in the same manner as the primary 

algal sample, except that only five scrapes were taken from 

rocks. The collected material was composited in a 125-mL 

bottle and shipped on dry ice to the USGS Kansas Organic 

Geochemistry Research Laboratory (OGRL) for analysis of 

microcystin concentrations.

Invertebrate samples were collected from RTH riffles, 

using a modified Surber sampler with 500-micrometer (μm) 

mesh net that samples a 0.25-m2 area of substrate (Moulton 

and others, 2002). The total invertebrate sample area was 

targeted at 12,500 cm2 (1.25 m2), the sum of a composite of 

five modified Surber samples each collected from a different 

section of riffle. The samples were sieved through a 500-μm 

sieve, large organic and inorganic debris was removed, and 

then samples were transferred to a 1-L bottle and preserved 

with 10-percent buffered formalin. Large or rare invertebrates, 

such as crayfish and large mollusks, were photographed and 

released in accordance with collection permit procedures. 

Identification and enumeration of invertebrate taxa (generally 

to either genus or species taxonomic levels) were completed 

by the NWQL.

A fish-community survey was conducted at each site by 

using a pulsed direct current backpack electrofishing unit in 

conjunction with generally two staff persons netting the fish. 

Two electrofishing passes of the sampling reach were made. 

Fish were collected by two crew members using 6-mm mesh 

nets, and fish from the first pass were held in live wells until 

the completion of the second pass. All fish were identified 

to species and counted in the field, then released back to the 

stream, except for some individuals that were retained either 

as voucher specimens or for analysis of mercury concentrations in fish tissue.

Fish Mercury Samples

Mercury concentrations in fish tissue were analyzed at 

92 of the 95 sites (table 2, in back of report), and mercury 

isotopes (indicators of potential Hg sources and environmental 

processing) were analyzed at 23 of the sites (table 2, in back 

of report). The 92 fish-tissue sites were not preselected; rather, 

the intent was to collect targeted fish species from every site 

where they were found; subsequently the targeted species were 

collected at 92 of the 95 sites. The 23 mercury isotope sites 

were selected on the basis of potential differences in mercury sources. Three general site types were selected: largely 

forested sites that were expected to receive Hg mainly from 

atmospheric deposition from distant sources, urban-industrial 

sites that were expected to have industrial (including legacy) 

Hg contamination, and urban-residential sites that were 

expected to have a mixture of sources. Mercury isotopes were 

analyzed in fish tissues and bed sediment samples collected 

from these 23 sites.

During the fish community survey (described previously), 

specimens of targeted species were retained for laboratory 

analysis of total mercury (THg) concentrations and stable 

isotopes of carbon (δ13C) and nitrogen (δ15N) and, at the 

23 isotope sites, mercury isotopes. The primary species that 

were targeted were small, midtrophic level, invertivorous 

fishes that are widely distributed across the NESQA study 

area, such as blacknose dace (Rhinichthys atratulus), longnose 

dace (R. cataractae), creek chub (Semotilus atromaculatus), 

and small-sized sunfish species (Lepomis spp.). Multiple target 

species were collected where possible. Each sample consisted 

of a single-species composite of 1 to 24 (median 10) similarly 

sized individual whole specimens. Secondarily, predatory 

game fish such as brook trout (Salvelinus fontinalis), brown 

trout (Salmo trutta), largemouth bass (Micropterus salmoides), 

and large specimens of sunfish species (Lepomis spp.) were 

retained when encountered. Each game fish sample consisted 

of an individual skinless fillet. Multiple samples of one or 

more game fish species were collected where possible.

Field processing was minimal for both the composite 

samples of whole midtrophic specimens and the fillet samples 

of individual game fish. Specimens that were retained for 

mercury and stable isotope analysis were field-rinsed in deionized water or native stream water (if deionized water was not 

available), placed in a plastic zip-lock bag (either individually or with other conspecifics), and frozen (on dry ice or in a 

field freezer). Samples were delivered to the USGS New York 

Water Science Center (NYWSC) laboratory where they were 

kept frozen until further processing. At the NYWSC laboratory, specimens were thawed, rinsed thoroughly in deionized 

water, and measured (total length). Game fish specimens 

were individually weighed, and a skinless fillet was removed 

as described in Scudder and others (2008). The fillet was 

triple-rinsed in deionized water, patted dry, weighed, placed in 

a fresh zip-lock bag, labeled, double-bagged, and frozen. Midtrophic-level fish specimens from each site were sorted into 

single-species composites (containing similarly sized individuals), rinsed thoroughly in deionized water, and batch-weighed 

(that is, all individuals in a composited sample were weighed 

together). All specimens in a composite sample were placed 

into a fresh zip-lock bag, labeled, double-bagged, and frozen.

Samples were shipped frozen on dry ice to either the 

Trace Elements Research Laboratory (TERL) at Texas 

A&M University in College Station, Texas (340 samples), 

or the USGS Mercury Research Laboratory (USGS Mercury 

Lab) in Middleton, Wisconsin (69 samples), for analysis of 

THg and percent moisture. The 69 samples submitted to the 

USGS Mercury Lab also were analyzed for stable isotopes 

of THg (δ202Hg, Δ199Hg, and Δ201Hg). Upon completion of 

processing and analysis at the TERL and the USGS Mercury 
Sample Collection and Processing 15

Lab, the remaining tissue (freeze-dried and homogenized) for 

each sample was sent to the Cornell University Stable Isotope 

Laboratory in Ithaca, N.Y., for analysis of stable isotopes of 

carbon (d13C) and nitrogen (d15N).

Sediment Samples

At each site during the ecological survey, sediment samples were collected from the streambed and the stream banks. 

At 14 sites prior to the start of the ecological surveys, two 

streambed sediment samples were collected during the second 

and sixth weeks of the 9-week QW sampling period. These 

additional samples were identified as “temporal bed sediment 

samples” and, in combination with results from samples collected during the ecological survey, were to be used to evaluate how sediment chemistry varied over the 9-week sampling 

period. These 14 sites are identified with “2” in the column 

labeled “Sediment Chemistry,” under “Ecological Surveys,” 

table 2 (in back of report).

Depending on the site, one or two streambed sediment 

samples were collected. A bulk sediment sample was collected 

at all sites for analysis of multiple constituents, including 

certain organic compounds, trace elements, organic carbon, 

and grain size. At 23 sites (mercury isotope sites), a second 

sediment sample was collected for analysis of total, methyl, 

and isotopic mercury. The bulk sediment sample collected at 

all sites and analyzed for multiple constituents was collected 

by following established USGS protocols (Shelton and Capel, 

1994; Radtke, 2005) with several collection method variations. 

Four-inch (about 10-cm) stainless steel cylinders and stainless 

steel spatulas were used to collect the sediment. Multiple collections of sediment were made from depositional areas along 

the 150-m ecological assessment reach, targeting locations 

where fine-grained sediments accumulated. Depositional zones 

across the reach were sampled in approximate proportion to 

their bottom surface area. The collection method required 

pushing the stainless steel cylinder into the streambed to a 

depth of 2 cm, then sliding the spatula under the cylinder to 

support the enclosed streambed core. Each streambed core was 

lifted gently out of the water to minimize the loss of fine material, and all cores were composited in a large plastic bucket; 

approximately 6 to 10 L of streambed material was collected 

for the sample. Samples were sieved in the field by using a 

2-mm stainless steel sieve that rested on top of the bucket.

The bulk sediment sample was placed on ice in the field 

and transported to a central processing facility at the USGS 

office in Troy, N.Y., where samples were homogenized and 

split into aliquots for various analyses. Each sample was 

homogenized by using a kitchen mixer with a stainless steel 

bowl and a bread-dough-style paddle operated at low speed. 

Prior to the NESQA sampling, testing was done with several streambed sediment samples to determine minimum 

mixing time to achieve a reasonably homogeneous sample; 

about 30 seconds was used for initial mixing and then about 

15 seconds for additional mixing between removal of aliquots. 

Sample aliquots were shipped chilled to various laboratories 

for toxicity testing and chemical analyses. Not all constituents 

were analyzed for all samples (appendix 1, table 1.1). Major 

and trace elements, organic carbon, radionuclides, and grain 

size were measured in samples from all sites. In samples 

from 72 sites, polycyclic aromatic hydrocarbons (PAHs) and 

other semivolatile compounds were measured. For 52 sites, 

among the 72 sites for which PAHs were measured, sediments 

were analyzed for organic wastewater indicators, organochlorine insecticides, polychlorinated biphenyls (PCBs), 

polybrominated diphenyl ethers (PBDEs), and current-use 

pesticides. Sediment from those 52 of the sites was tested by 

using standard whole-sediment toxicity tests with amphipod 

crustaceans (Hyalella azteca; 28-day exposures), midge larvae 

(Chironomus dilutus; 10-day exposures), and freshwater mussels (Lampsilis siliquoidea; 28-day exposures) to measure 

potential effects of contaminants on survival and growth. Toxicity testing was conducted at the USGS Columbia Environmental Research Center (CERC).

Aliquots for assessing the concentration of THg at all 

sites were taken from the bulk sediment samples, as described 

above. Sediment samples for Hg isotopes were collected 

separately at 23 sites with a cut-off 50-mL plastic syringe 

to extract plugs of sediment. The plugs were collected from 

6 to 10 depositional locations within and (or) near the stream 

reach and were placed into a wide-mouth plastic jar. Large 

pieces (such as twigs, leaves, and rocks) were removed from 

the sample by gloved fingers, and samples were immediately 

frozen. Samples were kept frozen and were shipped to the 

USGS Mercury Research Laboratory for analysis of total 

mercury concentration and mercury isotope analysis (the latter 

only in samples from the subset of 23 sites).

The bank sediment sample was collected from 5 to 

10 locations along the ecological sampling reach where an 

exposed or eroding bank was observed on either side of the 

stream. At each location, sediment was collected by using 

a precleaned plastic trowel to scrape a vertical furrow from 

above the water line to the top of the exposed bank (about 

1-cm depth into the bank). The bank scrapes were composited 

as a single sample in a 1-L plastic jar, which was stored on wet 

ice and shipped to the USGS Maryland-Delaware-D.C. Water 

Science Center in Baltimore, Maryland, for further processing 

and analysis of elements and radionuclides.

Physical Habitat

The physical habitat of the reach was characterized 

generally by following USGS protocols (Fitzpatrick and others, 1998). The 150-m sampling reach was segmented with 

11 primary transects that were set apart every 15 m along the 

reach and with 10 secondary transects that were set approximately midway between the primary transects. Descriptive and 

quantitative measurements were collected across each primary 

transect and included geomorphic channel unit type (that is, 

pool, riffle, or run), stream depth, substrate size at five locations (right and left edges of water, the center of the channel, 

and midway between channel edges and channel midpoint), 
16 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

stream wetted width, bank height, canopy cover at mid-transect, macrophyte coverage, and the presence of bars, islands, 

and potential fish habitat features. Measurements made across 

the secondary transects were wetted width and substrate size at 

the five locations described above. The surface water gradient 

was measured over the entire 150-m reach and indicated the 

average slope from the top to the bottom of the reach.

Sample Analyses

Most of the analyses of water, sediment, and invertebrate 

samples were conducted by the NWQL (appendix 2, tables 2.1 

to 2.10), and the methods are briefly described in this section. Analytical results from the NWQL were uploaded to 

the Water-Quality System (QWDATA) database within the 

National Water Information System (NWIS) of the USGS for 

storage and archiving. Results of each sample in QWDATA 

were uniquely identified by station identification number, date, 

time, and medium code. Additionally, each NESQA sample 

was labeled with a unique barcode as a backup sampletracking identifier. Real-time data recorded by data-logging 

instruments and by USGS staff in the field, such as streamflow, temperature, and biological-community data, are also 

discussed in this section; no laboratory analyses were required 

to generate these data, so they were processed at the USGS 

water science centers that operated the instruments or made 

the measurements.

Continuous Water Temperature and Streamflow

Discharge data collected at active USGS streamgages 

(54 sites) were continuously uploaded to and made available 

through the USGS NWIS database. For sites where pressure 

transducers were installed (41 sites), the raw stage data were 

processed with the HOBOware graphing and analysis software 

(Onset Computer Corporation, Bourne, Mass.). This process 

included applying corrections to the stage values with barometric pressure readings and comparing tape-down measurements from the reference point to the water surface to ensure 

that the instruments functioned consistently and reliably while 

they were in service.

The water temperature data were also processed with 

the HOBOware software; values were checked for outliers that could indicate that the data logger was out of water, 

such as with very low-flow conditions. This evaluation was 

particularly important because of the drought conditions that 

existed over much of the NESQA region during the summer 

of 2016. The general procedure used to assess the validity of 

temperature readings that appeared inordinately high was to 

first review streamflows at the site to determine if the high 

temperature values corresponded to minimal stage values, then 

compare these temperature values with those of nearby sites 

to assess if the data logger was reading air rather than water 

temperature. Erroneous water temperature data were subsequently deleted from the data file.

Chemical Analyses of Water, Sediment, and Fish

Discrete Water-Quality Samples

Water-quality samples collected over the 9- and 4-week 

QW sampling periods were analyzed for nutrients, major 

ions, DOC/ultraviolet absorbance (UVA), and pesticides by 

the NWQL with the exception that pesticides were analyzed 

in only the last sample collected (week 9) at eight of the 

forested and three of the tier 1 urban sites. Samples for major 

ions and nutrients were analyzed by the NWQL as specified 

in appendix 2 (tables 2.1 and 2.2). Total phosphorus concentrations were determined by colorimetry according to EPA 

method 365.1 (O’Dell, 1993). Dissolved ammonia, nitrite, and 

orthophosphate colorimetric analyses are described by Fishman (1993). Dissolved nitrate-plus-nitrite concentrations were 

determined by low-level enzyme reduction colorimetry with 

an automated discrete analyzer, as described by Patton and 

Kryskalla (2011). Concentrations of dissolved cations were 

determined by inductively coupled plasma-atomic emission 

spectroscopy (Fishman, 1993), and concentrations of dissolved 

anions were determined by ion chromatography, as described 

by Fishman and Friedman (1989).

Pesticides were analyzed by direct aqueous injection 

(DAI) liquid chromatography tandem mass spectrometry 

(LC–MS/MS) (appendix 2, table 2.3; Sandstrom and others, 

2015). The pesticide analytical method quantified 225 pesticides and pesticide degradates in filtered water samples. The 

targeted pesticides represent a broad range of chemical classes 

and were selected on the basis of criteria such as current-use 

intensity, probability of occurrence in streams and groundwater, toxicity to humans or aquatic organisms, and precision of 

analytical methods. The method uses direct aqueous injection 

of a 100-microliter (μL) sample onto the LC–MS/MS without 

any sample preparation other than filtration. Samples were 

analyzed with two injection modes—positive electrospray 

ionization (ESI) and negative ESI—using dynamic multiple 

reaction monitoring (MRM) conditions and with two MRM 

transitions for each analyte. Recoveries for most analytes 

ranged from 80 to 120 percent in the water types tested, 

with relative standard deviations of less than 30 percent. The 

method detection limits ranged from 1 to 103 nanograms per 

liter (ng/L) for 182 analytes analyzed in the ESI positive mode 

and from 2 to 106 ng/L for 42 analytes analyzed in the ESI 

negative mode. The remaining analytes (five) had method 

detection limits between 100 and 250 ng/L.

Human-use pharmaceuticals and organic wastewater 

indicator compounds were analyzed three times at the 9-week 

sites and once at the 4-week sites (appendix 1, table 1.1). Pharmaceutical samples were syringe-filtered into 20-mL vials, 

and organic waste indicator samples were collected as whole 

water samples into a 1-L baked amber glass bottle. Samples 

were analyzed for 112 pharmaceuticals by DAI LC–MS/MS 
Sample Analyses 17

(appendix 2, table 2.4; Furlong and others, 2008, 2014) and 

for organic wastewater indicator compounds by gas chromatography mass spectrometry (GC/MS) (appendix 2, table 2.5; 

Zaugg and others, 2006).

Stable nitrogen (15N) and oxygen (18O) isotopes of nitrate 

were analyzed in two of the weekly samples collected from 

the 9-week sites and in one of the weekly samples collected 

from the 4-week sites (appendix 1, table 1.1). Samples were 

filtered into bottles and frozen until nitrate concentration data 

were received and then shipped to the USGS Reston Stable 

Isotope Laboratory in Reston, Virginia. Isotopic analyses were 

done by following the method of Coplen and others (2012). 

Dissolved nitrate in water is converted to nitrous oxide (N2O) 

by denitrifying bacteria, and the nitrous oxide is analyzed for 

nitrogen and oxygen isotopic abundance by continuous-flow 

isotope-ratio mass spectrometry.

Methylmercury and THg concentrations in whole water 

were analyzed at the USGS Mercury Research Laboratory in 

Middleton, Wis., in five of the weekly samples collected from 

the 9-week sites and in three of the weekly samples collected 

from the 4-week sites. Methylmercury was analyzed by gas 

chromatographic separation with cold vapor atomic fluorescence spectrometry (DeWild and others, 2002); THg was 

analyzed by oxidation, purge and trap, and cold vapor atomic 

fluorescence spectrometry (method 1631, revision E; U.S. 

Environmental Protection Agency, 2002). The USGS Mercury 

Lab also analyzed DOC in samples collected weekly, as well 

as ultraviolet absorbance at 254 nanometers (UVA254) in the 

samples collected concurrently with the mercury samples.

Weekly filtered water samples were analyzed for 

glyphosate by using an enzyme-linked immunosorbent assay 

(ELISA) at the USGS Texas Water Science Center (Mahler 

and others, 2017). Glyphosate also was sampled during 

weeks 2 (at 59 sites) and 9 (at all sites) and analyzed at the 

Kansas OGRL by using an online solid-phase extraction and 

liquid chromatography/tandem mass spectrometry (Meyer and 

others, 2009). These data were used to evaluate quality control 

of the data analyzed by the ELISA method.

Weekly discrete whole-water samples were analyzed for 

suspended-sediment concentrations at the USGS Kentucky 

Sediment Laboratory in Louisville, Kentucky. Methods for 

processing suspended-sediment concentrations are described 

in Guy (1969) and Knott and others (1993) and included use 

of wet-sieving filtration.

A separate water sample was collected at all sites during 

week 8 to survey across the region for the concentrations of 

microcystin in streams (appendix 1, table 1.1). These samples 

were processed and analyzed by the Kansas OGRL following methods outlined in Loftin and others (2016). Unfiltered 

samples were lysed by three sequential freeze-thaw cycles at 

−20 degrees Celsius and 25 degrees Celsius and then syringe 

filtered through 0.7-micrometer glass fiber filters and frozen until analysis. Algal toxins were quantified by using the 

microcystin ELISA method with a minimum reporting level of 

0.10 micrograms per liter.

Pesticides From the Small-Volume Pesticide 

Automated Samplers

Daily-composite samples from the pesticide autosamplers (vials 1 through 7) were analyzed for pesticide concentrations by the EPA Office of Pesticide Programs (OPP) 

Analytical Chemistry Laboratory in Fort Meade, Md. Sample 

splits of the weekly composite sample (vial 9) and the spike 

sample (vial 8) were analyzed for pesticide concentrations by 

the NWQL in Denver, Colo., as well as the OPP laboratory. 

The NWQL analyzed the sample for current-use pesticides 

(appendix 2, table 2.3) following the methods described above 

(Sandstrom and others, 2015). The OPP laboratory used the 

same direct aqueous-injection LC–MS/MS method and instrument (Agilent Model 6460) used by the NWQL with similar 

detection levels

Polar Organic Compound Integrative Samplers

The POCISs were processed for analysis of pesticides 

and pharmaceuticals by the methods described in Alvarez 

(2010) and in Van Metre, Alvarez, and others (2017). The 

CERC eluted the concentrated extract from the field and 

blank POCIS using methanol and concentrated the extracts 

to 1 milliliter (mL). Concentrated extracts were sealed in 

1-mL amber glass ampules, stored at −20 °C, and shipped 

to the NWQL in Denver, Colo., for analysis. At the NWQL, 

the extracts were transferred to analytical vials and diluted 

1:100, which was required to prevent ionization suppression or 

enhancement of internal standards by the POCIS extracts during LC–MS/MS analysis. Laboratory blank and lab-fortified 

spike samples were prepared by using comparable volumes of 

methanol and processed with the POCIS extracts. The extracts 

were analyzed for concentrations of current-use pesticides 

(appendix 2, table 2.3) and pharmaceuticals (appendix 2, 

table 2.4) by LC–MS/MS by following the methods described 

previously for the discrete water samples.

Sediment Samples

An aliquot of each composited streambed sediment sample was analyzed for organic wastewater indicator compounds 

by using accelerated solvent extraction (ASE), solid-phase 

extraction cleanup, and GC/MS (appendix 2, table 2.6; Burkhardt and others, 2006). Sixteen parent PAHs were analyzed 

at RTI Laboratories (Livonia, Michigan, http://rtilab.com/), 

following EPA method 8270D (U.S. Environmental Protection Agency, 2014) with extraction by ASE and analysis by 

GC/MS with selected ion monitoring (appendix 2, table 2.7). 

A custom method was used for selected organohalogens in 

sediment (chlorinated and brominated compounds including insecticides, PCBs, and PBDEs), which extracted the 

sample by ASE, followed by solid-phase extraction cleanup 

and analysis by electron-capture negative ionization mode 

GC/MS with selected ion monitoring (appendix 2, table 2.8; 
18 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

reported in Mahler and others, 2009; Wagner and others, 

2014). Streambed sediment was analyzed for 118 current-use 

pesticides at the USGS Organic Chemistry Research Laboratory (Sacramento, California) by gas chromatography-tandem 

mass spectrometry (GC–MS/MS) (Hladik and McWayne, 

2012). Hormone compounds in sediment were analyzed with 

the use of GC–MS/MS (appendix 2, table 2.9; Foreman and 

others, 2012).

Major and trace elements were analyzed in an aliquot of 

the streambed sediment sample (2-mm sieve) and in an aliquot 

sieved to less than 63 micrometers (<63 μm). Bank sediment samples and Walling tube samples also were sieved to 

<63 μm, and the fine fraction was analyzed for major and trace 

elements. The samples were analyzed by AGAT Laboratories 

(Mississauga, Ontario, Canada, http://www.agatlabs.com/

index.cfm), using inductively coupled plasma-optical emission 

spectroscopy and inductively coupled plasma-mass spectrometry following dissolution in a mixture of hydrochloric, nitric, 

perchloric, and hydrofluoric acids (similar to the method 

documented in Smith and others, 2013). Aliquots of the 

streambed, bank, and Walling tube samples sieved to <63 μm 

were analyzed for radionuclides (lead-210, radium-226, 

cesium-137, and beryllium-7) at a USGS Sediment Radioisotope Laboratory in Menlo Park, Calif. Radionuclides were 

analyzed by using a high-resolution gamma spectrometer with 

an intrinsic germanium detector following methods described 

in Van Metre and others (2004).

Bed sediment samples from all sites were analyzed for 

THg and organic carbon at AGAT Laboratories. The mercury 

analysis was done by continuous flow-cold vapor-atomic 

fluorescence spectrometry (Hageman, 2007). Bed sediment 

samples that were collected from depositional zones from the 

23 isotope sites were analyzed for THg by the USGS Mercury 

Lab by direct combustion and atomic absorption detection 

following EPA method 7473 (U.S. Environmental Protection Agency, 1998). Loss-on-ignition was analyzed by the 

USGS Mercury Lab by the method in Fishman and Friedman 

(1989). Bed sediment samples from 23 isotope sites also were 

analyzed by the USGS Mercury Lab for Hg isotopes by the 

same methods as described previously for fish (“Fish Mercury 

Samples” subsection of “Sample Collection and Processing”), 

except that the bed sediment samples were digested in aqua 

regia (3:1 HCl:HNO3; Estrade and others, 2010; Lepak and 

others, 2015).

Periphyton Samples for Assessing Algal 

Productivity

Periphyton samples that were collected from five algalproductivity sites and processed in the field onto 0.47-μm 

glass-fiber filters were shipped to the NWQL for analysis of 

chlorophyll a and ash-free dry mass (AFDM). These samples 

were analyzed by using USGS method B–3520–85 and EPA 

method 445.0, respectively (appendix 2, table 2.10; Britton 

and Greeson, 1987; Arar and Collins, 1997). Ancillary data 

for assessing algal productivity were collected continuously 

by the PAR meter, YSI EXO2, and Sea-Bird SUNA continuous water-quality monitors and were processed into data 

records by the USGS water science centers that operated 

the instruments.

Ecological Surveys

Aquatic Biota

Periphyton samples for chlorophyll a, pheophytin a, and 

algal ash-free dry mass were collected during the ecological 

survey and processed in the field by filtering onto 0.47-μm 

glass-fiber filters. The filters were analyzed by using USGS 

method B–3520–85 and EPA method 445.0, respectively, 

by the NWQL (appendix 2, table 2.10; Britton and Greeson, 

1987; Arar and Collins, 1997).

Periphyton samples preserved with formalin were 

analyzed for diatom community composition and abundance 

at the INSTAAR laboratory, at the University of Colorado 

Boulder, following NAWQA protocols (Charles and others, 

2002) with the following modification. Four replicate slides 

of the diatoms were made by using Battarbee chambers to 

obtain random distribution of cells on cover slips (Battarbee, 

1973). A precount collection of voucher flora was created 

based on examination of 80 percent of the algal slides. The 

voucher flora included images of all taxa encountered, with 

a greater number of images for rare and previously unknown 

taxa. The images were sorted into operational taxonomic units 

(OTUs) and assigned OTU codes. Samples and their order of 

analysis were randomly assigned to two analysts. Ten percent 

of samples were reanalyzed by each analyst, and 10 percent 

of samples were analyzed in cross comparison. Finally, OTU 

codes were translated into formal scientific names following 

the taxonomy in the USGS BioData program and Diatoms 

of the United States (Spaulding and others, 2010). Voucher 

slides, digested material, and the voucher flora were archived 

at INSTAAR. The soft algae fractions of the samples were 

stored at INSTAAR for possible analysis at a later time.

Benthic invertebrate samples were processed by the 

Biological Unit of the NWQL using the quantitative fixed 

count method (Moulton and others, 2000). Briefly, the sample 

is sorted to attain a minimum of 300 organisms, which are 

then identified to the lowest possible taxonomic level (generally the species or genus level), which is similar to the method 

described in the EPA Rapid Bioassessment Protocol III 

(Barbour and others, 1999). Additionally, the biomass of 

arthropods and mollusks in the sample was estimated by 

measuring each of these organisms to the nearest millimeter 

and calculating their mass with the use of length-mass regressions for the various taxa. Quality assurance was verified 

in both the sorting step and the taxonomic step by a second 

person repeating these steps for 10 percent of the organisms. 

Taxonomic and enumeration results were uploaded to BioData 

(MacCoy, 2011).
Quality Assurance and Quality Control 19

Fish community data were based on species identification and counts made in the field, and the data were uploaded 

to BioData. Although most fish were returned to the streams, 

some individuals were retained either as voucher specimens 

for identification or for tissue samples that would be analyzed 

for Hg concentrations. In some cases, photographs were taken 

for verification of the field identification. Voucher specimens 

were submitted to the Biological Survey Laboratory of the 

New York State Museum in Troy, N.Y., for verification of field 

identifications and for archiving.

Sediment Toxicity Testing

Methods used for sediment toxicity testing are described 

in Moran and others (2017). For sediment testing, methods in 

U.S. Environmental Protection Agency (2000) and in American Society for Testing and Materials International (2014b) 

were followed; for mussel testing, methods in American 

Society for Testing and Materials International (2014a) were 

followed. Whole sediment toxicity tests were conducted with 

the amphipod Hyalella azteca (28-day exposures), with the 

midge Chironomus dilutus (10-day exposures), and with the 

mussel Lampsilis siliquoidea (28-day exposures). Up to 1.8 L 

(assuming a 50/50 split of solids and liquids) of the composited streambed sediment was used for toxicity testing. Testing 

for each species included endpoints of survival, weight, and 

biomass of test organisms. Exposures were conducted at 23 °C 

in 300-mL beakers containing 10 test organisms fed daily and 

100 mL of sediment with two volume additions per day of 

overlying water.

Physical Habitat

Data collected from habitat surveys were recorded on 

electronic field forms; these data were reviewed in the office 

by USGS staff. Any values on the field forms that were 

suspect (such as typographical errors) were resolved, and the 

data were loaded into the USGS BioData biological database 

(https://aquatic.biodata.usgs.gov).

Quality Assurance and Quality Control

This section primarily describes details of the quality 

assurance (QA) and quality control (QC) procedures for the 

collection of environmental water samples that were processed 

by the NWQL. QA/QC of project data is an iterative process 

that begins when samples are collected and continues through 

the establishment of sample records in NWIS and until the 

final acceptance of data as reviewed and approved or, in rare 

cases, rejected. This process allows for a continuous review of 

records by field personnel, RSQA data managers, lab analysts, 

team QW specialists, and team leads for both sample data 

(results) and metadata. Specific database scripts were developed to check sample coding logic and to generate data tables 

in multiple formats for data review and conformation. For 

sediment and fish samples, QA/QC procedures generally 

were simpler and included the use of replicates and standard 

reference materials during sample analyses in the laboratory. 

For samples analyzed at laboratories other than the NWQL, 

general QA/QC procedures may be found in the methods 

descriptions of publications cited previously in the “Sample 

Analyses” section and in the standard operating procedures 

maintained by the laboratories.

QA/QC procedures maintain the integrity, accuracy, and 

legal defensibility of results from data collection and assessment. Documented USGS QA/QC policies and procedures 

for environmental sampling were implemented in the NESQA 

study to ensure that the data can be interpreted properly and 

are scientifically defensible (Mueller and others, 1997; U.S. 

Geological Survey, 2006). QC samples were collected to 

identify, quantify, and document bias and variability in data 

that result from the sampling procedure (through field QC 

sampling) and laboratory procedures (through laboratory QC 

sampling). Field QC sampling captures bias and variability 

from sample collection, processing, shipping, and handling of 

samples. Laboratory QC sampling documents the variability of 

analytical methods and sample preparation in the laboratory. 

The QA/QC methods used by the NWQL for stream water 

analyses are described here. Methods used by the other laboratories that analyzed other NESQA samples may be found on 

the laboratory websites.

To ensure that all field crews followed consistent sample 

collection and processing procedures, classroom training 

was held for field personnel prior to the sampling period. In 

addition, all personnel worked through a full suite of sample 

collection and sample processing procedures at one of the 

NESQA sites prior to the start of the weekly sampling period. 

To minimize potential confusion in the field, all sampling 

scheduling, creation of analytical services request forms 

(ASRs) and bottle labels, and preparation of bottle kits (all 

sample containers needed for each site for a given visit) were 

handled centrally by USGS personnel who had provided similar support to previous RSQA studies.

The QC samples for constituents measured in water 

included field blanks, matrix spikes, and replicates (table 4; 

appendix 1, table 1.1). The QC plan was designed not only 

to meet or exceed 5 percent QC samples for inorganics and 

10 percent for organics but also to ensure that QC was distributed across the region evenly and that every field crew was 

assigned QC samples at an appropriate interval. Field blanks 

were used to test if cleaning procedures would adequately 

remove any sampling equipment contamination introduced 

by samples obtained at previous sites and ensure that sample 

collection, processing, handling, and shipping did not result 

in contamination (Mueller and others, 1997; U.S. Geological 

Survey, 2006). Field replicates were used to test the precision 

of analyses at the laboratory and were prepared by dividing 

a single volume of water into two samples in the field. When 

these samples were collected from the churn, either filtered 

or not, two containers were filled sequentially. When grab 
20 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

Table 4. Summary counts of environmental, field blank, replicate, and spike samples of stream water from the 95 stream sites 

sampled in the Northeast Stream Quality Assessment of the U.S. Geological Survey National Water-Quality Assessment Project in 2016. 

[Recommended percentages are from Mueller and others (1997). QA, quality assurance; KS OGRL, U.S. Geological Survey Kansas Organic Geochemistry 

Research Laboratory; N/A, not applicable; --, no data]

Laboratory schedule Type of sample Sample counts

Ratio of QA to environmental samples

(percent)

Actual Recommended

Major ions Environmental 675 N/A N/A

Blank 23 3.4 a1.6

Replicate 30 4.4 a1.6

Spike 0 0 0

Nutrients Environmental 693 N/A N/A

Blank 23 3.3 a1.6

Replicate 29 4.2 a1.6

Spike 0 0 0

Dissolved organic carbon Environmental 682 N/A N/A

Blank 22 3.2 a1.4

Replicate 28 4.1 a1.4

Spike 0 0 0

Pesticides Environmental 640 N/A N/A

Blank 24 3.8 a1.4

Replicate 28 4.4 a1.4

Spike 62 9.7 b9.1

Glyphosate (immunoassay) Environmental 671 N/A N/A

Blank 23 3.4 --

Replicate 28 4.2 --

Spike 0 0 --

Pharmaceuticals Environmental 212 N/A N/A

Blank 10 4.7 --

Replicate 11 5.2 --

Spike 10 5 --

Organic wastewater indicators Environmental 211 N/A N/A

Blank 10 4.7 --

Replicate 10 4.7 --

Spike 11 5.2 --

Glyphosate (KS OGRL) Environmental 118 N/A N/A

Blank 6 5.1 --

Replicate 7 5.9 --

Spike 6 5.1 --

Mercury Environmental 401 N/A N/A

Blank 21 5.2 a1.4

Replicate 23 5.7 a1.4

Spike 0 0 0

Isotopes Environmental 153 N/A N/A

Blank 0 0 --

Replicate 14 9.2 --

Spike 0 0 -- a

Mueller and others (1997) recommend substituting 1 of the indicated sample types per month if many environmental samples are collected in a short period 

of time rather than a set of 1 per 30 (3.3 percent) or 1 per 20 (5 percent). Therefore, for the Northeast Stream Quality Assessment study, weekly samples were 

collected at 59 sites for 9 weeks, so the recommended percentage was computed as 1 monthly quality control sample at 59 sites, or 1.4 percent.

b

Recommended amount is one per site.
Water-Quality Data-Management Procedures 21

samples were collected, replicates were collected sequentially 

directly from the stream. These replicates provided a measure 

of the variability introduced during sample processing and 

analysis (Mueller and others, 1997; U.S. Geological Survey, 

2006). Field and laboratory matrix spikes were used to assess 

the potential bias for analytes in a particular sample matrix. 

Bias is estimated from spiked samples by calculating the 

percentage of the added analyte (spike material) measured 

(recovered) in the sample at the laboratory (Mueller and others, 1997; U.S. Geological Survey, 2006). Recovery can be 

either greater than or less than 100 percent, so the bias can be 

either positive or negative; however, matrix interference and 

analyte degradation generally result in a negative bias.

Field blanks were collected once from 22 to 24 sites for 

each of the basic laboratory schedules (major ions, nutrients, dissolved organic carbon, pesticides, and glyphosate by 

immunoassay) sampled weekly (table 4). For QA/QC samples 

collected as part of NAWQA, Mueller and others (1997) recommend 1 field blank or replicate per every 30 (3.3 percent) 

or 20 (5 percent) environmental samples for the previously 

mentioned constituents when sampling at long-term sites; 

however, if many environmental samples are collected in a 

short period of time, as was the case in the NESQA study, it 

is recommended to lower the QC sample frequency to 1 per 

month. Therefore, for the NESQA study, the recommended 

percentage was computed as 1 monthly QC sample at 59 sites, 

or 1.4 percent. Actual field blanks represented 3.2 to 3.8 percent of the environmental samples, and split replicates for the 

same analyses represented 4.1 to 4.4 percent of the environmental samples, which met the frequency recommendation 

(table 4; Mueller and others, 1997).

No recommendation for QA/QC samples was provided 

for the organic compounds of emerging concern (pharmaceuticals and organic wastewater indicators) in Mueller and 

others (1997); therefore, we applied the same approach as 

used for pesticides. For pharmaceutical and organic wastewater indicator analyses, field blanks represented 4.7 percent of 

the environmental samples, and split replicates represented 

5.2 and 4.7 percent of the environmental samples, respectively 

(table 4). Matrix spikes were performed on all analyses for 

organic compounds, with the exception of glyphosate analysis 

by immunoassay. The frequency of these spikes ranged from 

5 to 5.2 percent, depending on the analyte (table 4).

Quality assurance included maintaining standardized 

sample collection and handling protocols among all field 

personnel as described in the National Field Manual (U.S. 

Geological Survey, variously dated) for water and sediment 

sampling and in Moulton and others (2002) for ecological 

sampling. All sampling and handling protocols were reviewed 

by field personnel involved in the NESQA study during training courses prior to field work. Additionally, several programs 

exist within the USGS Quality Systems Branch to help document the quality of project results. For laboratory analyses 

conducted by the NWQL, documented QC included doubleblind analyses of blanks for organic and inorganic constituents and provision of graphical and tabular control data for 

the analytical lines. Field personnel involved in the NESQA 

study are tested annually to verify their proficiency in collecting field data, including temperature, pH, dissolved oxygen, 

alkalinity, and specific conductance.

Water-quality data from each sampling event were 

reviewed for completeness, precision, bias, and transcription errors when received from the laboratory as part of the 

QA/QC procedures. Water-quality and sediment-quality 

data were stored in the NWIS database. Quality-assured 

water-quality and sediment-quality data are available for 

retrieval at https://waterdata.usgs.gov/nwis/sw and through 

the data retrieval application at the RSQA project website 

(https://webapps.usgs.gov/RSQA/). The NWQL provides 

all QA/QC documentation for their analytical services at 

http://nwql.usgs.gov/Public/quality.shtml.

Water-Quality Data-Management 

Procedures

An important goal of data management for the NESQA 

study is to have the data reviewed, approved, and stored in a 

USGS approved database that is appropriate for the specific 

type of data (for example, water quality, streamflow, biological). Because NESQA sampling sites were located in multiple 

States, data entry and retrieval for sites in a particular State 

were managed by the USGS water science center (WSC) for 

that State. The NWIS station number that is used to identify 

a site (table 1, in back of report) is the master indexing and 

retrieval element for accessing data specific to the site. The 

NWIS database is the repository for most of the water-quality 

and streamflow data, which are the majority of the NESQA 

data, and is composed of separate distributed databases that 

are each hosted by the WSC for the State in which the site is 

located. Thus, the WSC responsible for managing NESQA 

data in NWIS depends on the State in which the NESQA site 

was located. Additionally, a data-management team was created to include both national RSQA staff and regional NESQA 

staff to facilitate the data-management process. Centralization 

of the data-management process was adopted to ensure consistency among the WSCs for each RSQA study and among all 

RSQA study areas. Nine main steps were implemented for the 

data-management process:

1. Sampling matrix and sample coding design

2. Electronic field form use, including barcoding

3. Sample status checks at all laboratories

4. NWIS sample record checks

5. Data transfer from laboratory to NWIS

6. Establishment of project networks

7. Sample coding and field parameter checks
22 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

8. Data quality checks

9. Approval of data in NWIS and other databases, 

as appropriate

Sites selected for the NESQA study were assigned the 

appropriate network designations in NWIS ProjectNetworks 

(Dupré and others, 2013) which allows integration with similar sites across many regions and designation of the site type 

in NWIS. These network designations were obtained from the 

project planning documents and, where possible, kept consistent with other network designations that may have been used 

in previous regional studies. ProjectNetworks documentation 

was provided to local WSC personnel so they could establish 

their sites in NWIS ProjectNetworks.

Prior to the start of sampling, the manager of the datamanagement team prepared a matrix that would be the 

sampling design and coding plan for all aspects of the field 

activities. The sampling matrix distributed QC samples 

approximately equally across sites, sample teams, and time 

periods for optimum coverage. The matrix also served as a 

summary diagram for the type, frequency, and location of 

environmental and QC samples to be collected (appendix 1, 

table 1.1). A sample coding scheme was developed by the 

data manager that was used by the NESQA sampling teams to 

ensure a well-structured and manageable dataset. Additionally, 

training and written guidelines for sampling coding were made 

available to sampling teams prior to the start of sampling.

Weekly sample bottle packs were assembled at a central 

location by a USGS staff person designated as the field-supply 

manager. The bottle packs consisted of the necessary bottles, 

filters, preservatives, labels, and analytical service requests 

(ASRs) for each stream site; the packs were shipped to the 

local WSC at least one week prior to sampling. Centralizing 

the distribution of sample bottle packs helped ensure that 

correct sample coding, sample schedules, and timing of QC 

samples matched the proposed sample plan and reduced errors 

in the sample login process at the analytical laboratories.

Most of the NESQA sampling teams used the Personal 

Computer Field Form (PCFF) version 7.2 software created 

by the USGS, which provides electronic field forms for data 

collection at sampling sites. However, the use of PCFF did 

not preclude the use of all paper field forms when sampling; 

a two-page standardized form for NESQA water-quality field 

notes was routinely used at all sites to record basic site conditions when samples were collected and to affix bar codes that 

identified the samples. The bar codes were unique identifiers 

used to associate specific sample types with a site and the 

sampling event. The PCFF software streamlines the process of 

uploading (logging in) field data and sampling codes to NWIS 

by automatically generating the batch load files required 

by NWIS (qwsample and qwresult), thereby improving the 

efficiency of data flow from field and laboratory to database. 

The information uploaded to NWIS for each sample is stored 

under a unique number associated with that sample, as are 

later results received from the laboratory. In addition, the 

automation of data upload to NWIS limits the incidence of 

transcription errors that may occur during the manual entry 

of data into NWIS. Although PCFF can be used to generate 

the NWQL ASR documents for samples being submitted to 

the NWQL, the field-supply manager provided ASRs to the 

sampling teams each week along with the corresponding bottle 

sets. Some field teams did not use the PCFF; in these cases, 

field data were recorded on paper field forms and then transferred onto electronic digital forms in the office.

Sample shipment schedules were established prior to the 

start of sampling for NESQA, and generally shipments were 

made twice per week (appendix 1, table 1.4). Sampling teams 

and other WSC personnel were responsible for the shipment 

process. The data manager continuously tracked the shipments to verify that the shipped samples were received at 

each laboratory (1) within the correct holding times, (2) in the 

proper condition (for example, chilled samples received at the 

appropriate temperature of 4 °C or less), and (3) with proper 

documentation. The data manager worked with the laboratories to correct problems with mislabeled samples or ASRs 

in a timely manner and to communicate problem-resolution 

approaches to WSC personnel. During this process, the data 

manager also established the connection between the USGS 

Laboratory Information Management System used to transfer 

sample results and the NWIS database used to receive and 

store sample results.

During sampling and the corresponding establishment 

of sample records in NWIS, the data manager inspected 

sample coding and procedures to ensure that sample records 

were established properly and in a consistent manner. Sample 

coding or procedures were modified if found to be inaccurate 

or inconsistent. These modifications involved changes or corrections to sample time offsets, sample type coding, or other 

documentation at the laboratory or in NWIS. Modifications in 

sample coding or procedures related to data management or 

sample submittal were communicated immediately to sampling teams to ensure that appropriate adjustments were made 

before the next sampling.

Most of the laboratories used for NESQA sample analysis 

transmitted sample results through the Water Quality Data 

Exchange (QWDX) for automatic upload into the NWIS database. For those laboratories without the ability to use QWDX, 

sample results were loaded into NWIS by using manually 

created batch files. Batch files were created by the data manager upon receipt of electronic data from the laboratory and 

were loaded into the respective WSC NWIS host by the data 

manager or the local database administrator for the WSC. The 

data manager verified that the batch files of data were properly loaded into NWIS. Data files provided through email by 

laboratories and data not applicable to NWIS (for example, 

CERC toxicity data) were stored electronically in the RSQA 

team database rather than NWIS. These data, and data such as 

quality assurance sample results not publicly available through 

NWIS, will be made available using the ScienceBase digital 

data repository supported by the USGS.

After sampling was completed, the data manager 

inspected the NWIS sample records for completeness 
Atlantic Highlands Flow-Ecology Study 23

regarding field data collection, including stream measurements (streamflow, stage, sampling points, stream width, and 

so forth), field parameters (pH, air and water temperature, 

specific conductance, dissolved oxygen), and sample coding (sample purpose, purpose of site visit, sampling method, 

sampler type, and multiple QC-related sample codes). Manual 

checks were made for each sample, and any corrections were 

communicated to WSC personnel; the data manager, WSC 

personnel, or database administrator made any needed changes 

in NWIS.

National RSQA staff scientists reviewed the water-quality 

and sediment-quality results received from the laboratory. 

The water-quality data reviews included identification and 

review of extremes in the data (outliers); inconsistencies or 

unexpected results in the data; and major differences between 

environmental samples and replicates, detected values in 

blanks, and analyte recoveries in spike samples. The RSQA 

staff scientists communicated requests for reruns, reloads, and 

verification of results from the laboratory; they worked closely 

with the data manager to verify completeness of sample 

results, and a final dataset was established in NWIS as well as 

in a central RSQA database.

Upon completion of the data review process by the 

RSQA staff scientists, the data manager provided tables of 

the data-review results to the respective analysts for internal reviews. WSC personnel who were responsible for data 

quality at the WSC changed the data quality indicator (DQI) 

code for each individual water-quality parameter, on the basis 

of the results of the review, to reviewed and accepted (R) or 

reviewed and rejected (Q). Any data that were rejected at the 

WSC level were not used in data analysis or publications. In 

addition to NWIS and ScienceBase, water quality, sediment, 

biological tissue, and ecological survey data are also made 

available at the RSQA mapping and data application website, which allows mapping, querying, and data downloads 

(https://webapps.usgs.gov/RSQA/#!/download).

Atlantic Highlands Flow-Ecology Study

Prior to the NESQA, a study was conducted in 2014 

to investigate the effects of flow alteration on the ecological 

condition of streams in the Northeast. Specific objectives were 

to (1) quantify the extent of flow alterations at USGS gaged 

streams across the Atlantic Highlands ecoregion; (2) identify 

streams where flow alterations likely have resulted in thermal 

regime shifts; and (3) describe how flow alterations are related 

to the health of aquatic ecosystems, as indicated by changes 

in the thermal regime, physical habitat, water chemistry, and 

aquatic biota. Unlike the NESQA study that was conducted as 

a multistressor investigation, the Atlantic Highlands flowecology study was primarily focused on flow alteration as a 

single stressor; thus, a different set of criteria was used for site 

selection that resulted in the study being more constrained in 

spatial extent and sampling elements.

To identify a network of sites for the study, a preliminary list of candidate streams was developed that met specific 

criteria: the streams were in the Atlantic Highlands ecoregion, 

were in primarily forested watersheds with less than 20 percent developed land, were outfitted with an active USGS 

streamgage, and had at least 10 years of antecedent streamflow 

data. A total of 190 candidate sites met these criteria. Geospatial data from the USGS GAGES–II dataset were used to 

identify the extent of flow alteration for the candidate sites 

with the use of an index of hydrologic alteration calculated 

from variables in the dataset (Falcone, 2011); sites then were 

selected to represent a gradient of hydrologic alterations from 

essentially unaltered (forested watersheds with no known 

streamflow modifications upstream from site) to highly 

altered (for example, immediately downstream from a large 

impoundment with regulated flows). Site reconnaissance was 

conducted during 2013 to identify a 150-m sampling reach, 

identify riffle habitat along the reach, evaluate access to the 

reach for sampling, and ascertain the absence of point sources 

and other human-related factors that could potentially confound verifying streamflow alteration as the primary stressor. 

After results from the reconnaissance were assessed, 66 gaged 

sites across the Atlantic Highlands ecoregion were deemed 

suitable for the study. Habitat was surveyed, and invertebrates 

and algae samples were collected at 60 “full ecology sites,” 

but only invertebrate samples were collected at 6 “invertebrate 

only sites” (table 5).

All 66 sites were instrumented with a water temperature data logger that was installed in the water column in the 

manner described previously for the NESQA study, except in 

cases where water temperature was already being collected as 

part of the data collection routine for a site; additionally, an 

air temperature data logger was installed at all sites near the 

stream reach (typically in a tree). The data loggers were programmed to collect data at hourly intervals and were deployed 

in August 2013. They were removed in the fall of 2014, after 

ecological sampling was completed, in order to characterize at 

least a full year of air and water temperature regimes at each 

site. Also, a bed sediment sample was collected from finegrained depositional zones within the stream reach of 41 sites 

during the visits when temperature sensors were deployed 

(table 5, see footnote). Sediment from the upper 2 cm of 

depositional substrate was collected from multiple locations 

by using an inverted glass petri dish and small Teflon square, a 

technique similar to that used for NESQA sediment sampling. 

Sediment from multiple locations in the reach was composited in a glass bowl and mixed thoroughly. Subsamples were 

then removed and placed into vials and jars appropriate to 

each intended analysis. Frozen subsamples were submitted to 

the USGS Mercury Research Laboratory for analysis of total 

mercury, methylmercury, and loss on ignition. Chilled (wet 

ice) subsamples were submitted to the NWQL for analysis of 

PAHs and halogenated compounds, to the USGS Crustal Geophysics and Geochemistry Laboratory for analysis of major 

and trace elements, and to the USGS Sediment Radioisotope 

Laboratory for analysis of radionuclides. Methods for each of 
24 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

Table 5. Stream watersheds that were included in the Atlantic Highlands flow-ecology study, conducted by the U.S. Geological 

Survey as part of the National Water-Quality Assessment Project in 2014.

[Full ecology sites included habitat surveys and algal and invertebrate samples, whereas the invertebrate-only sites did not include habitat surveys and algal 

samples. Sites with NWIS station numbers shaded were also part of the Northeast Stream Quality Assessment site network. Latitude and longitude are 

referenced to the North American Datum of 1983 and shown in decimal degrees. States are abbreviated with two-letter postal codes; for example, NH is New 

Hampshire. NWIS, U.S. Geological Survey National Water Information System database; km2, square kilometer]

NWIS 

station 

number

NWIS station name Field identifier Latitude

(NWIS)

Longitude

(NWIS)

Drainage 

area

(km2)

Full ecology sites

01052500 DIAMOND RIVER NEAR WENTWORTH LOCATION, NH NH_DIAMO_WL 44.8774 -71.0575 384

01054200 WILD RIVER AT GILEAD, MAINE ME_WILDR_GI 44.3904 -70.9796 181

01055000 SWIFT RIVER NEAR ROXBURY, MAINE ME_SWIFT_RO 44.6427 -70.5888 251

01064801 BEARCAMP RIVER AT SOUTH TAMWORTH, NH NH_BEARC_ST 43.8301 -71.2878 173

01075000 PEMIGEWASSET RIVER AT WOODSTOCK, NH NH_PEMIG_WO 43.9762 -71.6795 504

01082000 CONTOOCOOK RIVER AT PETERBOROUGH, NH NH_CONTO_PE 42.8626 -71.9592 175

01133000 EAST BRANCH PASSUMPSIC RIVER NEAR EAST HAVEN, VT VT_EBPAS_EH 44.6339 -71.8976 138

01134500 MOOSE RIVER AT VICTORY, VT VT_MOOSE_VI 44.5117 -71.8373 195

01135150 POPE BROOK (SITE W-3) NEAR NORTH DANVILLE, VT VT_POPEB_ND 44.4762 -72.1245 10

01135300 SLEEPERS RIVER (SITE W-5) NEAR ST. JOHNSBURY, VT VT_SLEEP_EF 44.4353 -72.0389 111

01137500 AMMONOOSUC RIVER AT BETHLEHEM JUNCTION, NH NH_AMMON_BJ 44.2687 -71.6304 229

01139800 EAST ORANGE BRANCH AT EAST ORANGE, VT VT_EORAN_EO1 44.0928 -72.3357 23

01153550 WILLIAMS RIVER NEAR ROCKINGHAM, VT VT_WILLI_RO1 43.1917 -72.4851 290

01154000 SAXTONS RIVER AT SAXTONS RIVER, VT VT_SAXTO_SA1 43.1376 -72.4881 187

01155500 WEST RIVER AT JAMAICA, VT VT_WESTR_JA 43.1090 -72.7754 460

01158600 OTTER BROOK BELOW OTTER BROOK DAM, NEAR KEENE, NH NH_OTTER_KE1 42.9459 -72.2368 122

01164000 MILLERS RIVER AT SOUTH ROYALSTON, MA MA_MILLE_SR 42.6298 -72.1504 492

01166500 MILLERS RIVER AT ERVING, MA MA_MILLE_ER1 42.5976 -72.4381 966

01169000 NORTH RIVER AT SHATTUCKVILLE, MA MA_NORTH_SH1 42.6384 -72.7251 231

01169900 SOUTH RIVER NEAR CONWAY, MA MA_SOUTH_CO1 42.5420 -72.6937 62

01170100 GREEN RIVER NEAR COLRAIN, MA MA_GREEN_CO1 42.7034 -72.6706 107

01174565 WEST BRANCH SWIFT RIVER NEAR SHUTESBURY, MA MA_WBSWI_SH1 42.4551 -72.3818 33

01175500 SWIFT RIVER AT WEST WARE, MA MA_SWIFT_WW1 42.2679 -72.3326 490

01179500 WESTFIELD RIVER AT KNIGHTVILLE, MA MA_WESTF_KN1 42.2879 -72.8643 422

01180500 MIDDLE B WESTFIELD RIVER AT GOSS HEIGHTS, MA MA_MBWES_GH1 42.2587 -72.8726 137

01181000 WEST BRANCH WESTFIELD RIVER AT HUNTINGTON, MA MA_WBWES_HU1 42.2373 -72.8957 244

01185500 WEST BRANCH FARMINGTON RIVER NEAR NEW BOSTON, MA MA_WBFAR_NB 42.0793 -73.0729 237

01186000 WEST BRANCH FARMINGTON RIVER AT RIVERTON, CT CT_WBFAR_RI1 41.9629 -73.0176 334

01187300 HUBBARD RIVER NEAR WEST HARTLAND, CT CT_HUBBA_WA 42.0373 -72.9390 54

01202501 SHEPAUG RIVER AT PETERS DAM AT WOODVILLE, CT CT_SHEPA_WO1 41.7193 -73.2929 100

01315500 HUDSON RIVER AT NORTH CREEK, NY NY_HUDSO_NC1 43.7009 -73.9835 2,059

01321000 SACANDAGA RIVER NEAR HOPE, NY NY_SACAN_HO1 43.3528 -74.2704 1,264

01333000 GREEN RIVER AT WILLIAMSTOWN, MA MA_GREEN_WI1 42.7090 -73.1968 112

01336000 MOHAWK RIVER BELOW DELTA DAM NEAR ROME, NY NY_MOHAW_RO1 43.2645 -75.4363 386

01343060 WEST CANADA CREEK NEAR WILMURT, NY NY_WCANA_WI1 43.3662 -74.9577 610
Atlantic Highlands Flow-Ecology Study 25

Table 5. Stream watersheds that were included in the Atlantic Highlands flow-ecology study, conducted by the U.S. Geological 

Survey as part of the National Water-Quality Assessment Project in 2014.—Continued

[Full ecology sites included habitat surveys and algal and invertebrate samples, whereas the invertebrate-only sites did not include habitat surveys and algal 

samples. Sites with NWIS station numbers shaded were also part of the Northeast Stream Quality Assessment site network. Latitude and longitude are 

referenced to the North American Datum of 1983 and shown in decimal degrees. States are abbreviated with two-letter postal codes; for example, NH is New 

Hampshire. NWIS, U.S. Geological Survey National Water Information System database; km2, square kilometer]

NWIS 

station 

number

NWIS station name Field identifier Latitude

(NWIS)

Longitude

(NWIS)

Drainage 

area

(km2)

Full ecology sites—Continued

01349810 WEST KILL NEAR WEST KILL, NY NY_WESTK_WK1 42.2304 -74.3929 74

01350080 MANOR KILL AT WEST CONESVILLE NEAR GILBOA, NY NY_MANOR_GI1 42.3770 -74.4129 84

01350140 MINE KILL NEAR NORTH BLENHEIM, NY NY_MINEK_NB1 42.4290 -74.4729 44

013621955 BIRCH CREEK AT BIG INDIAN, NY NY_BIRCH_BI1 42.1090 -74.4518 33

01362200 ESOPUS CREEK AT ALLABEN, NY NY_ESOPU_AL1 42.1170 -74.3801 169

01363382 BUSH KILL BLW MALTBY HOLLOW BK AT WEST SHOKAN, NY NY_BUSHK_WS1 41.9656 -74.2929 44

01374581 W BR CROTON RIVER BELOW DAM NEAR KENT CLIFFS, NY NY_WBCRO_KC1 41.4498 -73.7365 58

01384500 RINGWOOD CREEK NEAR WANAQUE, NJ NJ_RINGW_WA1 41.1275 -74.2656 44

01413398 BUSH KILL NEAR ARKVILLE, NY NY_BUSHK_AR1 42.1509 -74.6013 121

01413408 DRY BROOK AT ARKVILLE, NY NY_DRYBR_AR1 42.1468 -74.6232 213

01414000 PLATTE KILL AT DUNRAVEN, NY NY_PLATT_DU1 42.1331 -74.6954 90

01414500 MILL BROOK NEAR DUNRAVEN, NY NY_MILLB_DU1 42.1062 -74.7304 64

01427510 DELAWARE RIVER AT CALLICOON, NY NY_DELAW_CA 41.7568 -75.0574 4,725

01434017 EAST BR NEVERSINK RIVER NR CLARYVILLE, NY NY_EBNEV_CL1 41.9254 -74.5402 60

01434025 BISCUIT BK ABOVE PIGEON BK AT FROST VALLEY, NY NY_BISCU_FV 41.9954 -74.5010 10

01434498 WEST BRANCH NEVERSINK R AT CLARYVILLE, NY NY_WBNEV_CL1 41.9204 -74.5746 88

01435000 NEVERSINK RIVER NEAR CLARYVILLE, NY NY_NEVER_CL 41.8901 -74.5899 172

01436000 NEVERSINK RIVER AT NEVERSINK, NY NY_NEVER_NE 41.8201 -74.6354 241

01436690 NEVERSINK RIVER AT BRIDGEVILLE, NY NY_NEVER_BR 41.6381 -74.6169 443

01439500 BUSH KILL AT SHOEMAKERS, PA PA_BUSHK_SH 41.0882 -75.0377 306

01440400 BRODHEAD CREEK NEAR ANALOMINK, PA PA_BRODH_AN1 41.0848 -75.2146 175

01447800 LEHIGH RIVER BLW FRANCIS E WALTER RES NR WHITE 

HAVEN, PA PA_LEHIG_WH1 41.1048 -75.7321 753

04287000 DOG RIVER AT NORTHFIELD FALLS, VT VT_DOGRI_NF1 44.1828 -72.6404 199

04288230 RANCH BROOK AT RANCH CAMP, NEAR STOWE, VT VT_RANCH_ST1 44.5039 -72.7818 10

04289000 LITTLE RIVER NEAR WATERBURY, VT VT_LITTL_WA1 44.3701 -72.7693 287

Invertebrate-only sites

01053500 ANDROSCOGGIN RIVER AT ERROL, NH NH_ANDRO_ER 44.7826 -71.1287 2,702

01054000 ANDROSCOGGIN RIVER NEAR GORHAM, NH NH_ANDRO_GO 44.4358 -71.1902 3,528

01055500 NEZINSCOT RIVER AT TURNER CENTER, MAINE ME_NEZIN_TC 44.2695 -70.2296 440

01144000 WHITE RIVER AT WEST HARTFORD, VT VT_WHITE_WH1 43.7142 -72.4181 1,790

04285500 NORTH BRANCH WINOOSKI RIVER AT WRIGHTSVILLE, VT VT_NBWIN_WR1 44.2995 -72.5787 182

04288000 MAD RIVER NEAR MORETOWN, VT VT_MADRI_MO 44.2773 -72.7426 364

1

A bed sediment sample was collected at these sites.
26 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

these analyses are described previously (section “Chemical 

Analyses of Water, Sediment, and Fish”).

Each of the 66 sites was visited twice during the summer of 2014 for data collection, generally using methods 

described for the NESQA study. The first visit, in August, 

consisted of the following at the 60 full ecology sites: measuring specific conductance, dissolved oxygen, pH, and water 

temperature with YSI field meters; collecting a grab water 

sample from a well-mixed portion of the stream (one sample 

per site, two additional QA samples at three sites); collecting 

invertebrate and periphyton samples from riffle habitats; and 

measuring the water-surface gradient along the reach. During the August 2014 visit at the six invertebrate only sites, an 

invertebrate sample was collected from riffle habitats, but no 

other sampling was done. The second site visit was made in 

late September or early October and consisted of the following: removing the temperature data loggers from the reach 

and downloading the data at all sites, and conducting a habitat 

assessment at the full ecology sites.

Water samples were kept on wet ice in the field and transferred to a refrigerator at the NYWSC laboratory. Samples 

were then shipped overnight to the NWQL and analyzed at 

the NWQL for major ions, dissolved organic carbon, acidneutralizing capacity, filtered aluminum, and inorganic 

monomeric aluminum, according to methods detailed in 

Lawrence and others (1995). Algal samples were preserved 

in formalin as previously described and were shipped to 

INSTAAR and analyzed as previously described. Invertebrate 

samples were field-processed and preserved as previously 

described. The samples were analyzed by a contract laboratory 

(Rhithron Associates, Inc., Missoula, Montana), and the data 

were uploaded into the USGS BioData biological database 

(https://aquatic.biodata.usgs.gov).

Summary

This report summarizes the design and methods used 

during an intensive regional study to assess stream quality in the northeastern United States: the Northeast Stream 

Quality Assessment. Ninety-five wadeable stream sites were 

selected throughout five Level III ecoregions to determine the 

occurrence and levels of multiple stressors and to assess the 

conditions of aquatic biological communities. Water quality was measured during a 4- or 9-week period from June to 

August 2016, followed by an ecological survey to assess the 

biological communities (algal, invertebrates, fish), contaminants in sediment, mercury in fish tissue, and the physical 

habitat of the stream, as well as other aspects of stream 

condition such as indicators of harmful algal blooms. Multiple parameters covering a wide variety of potential stressors 

to aquatic life were measured during the Northeast Stream 

Quality Assessment and included both discrete and continuous 

data collected over the course of the assessment at all 95 sites 

and in special focused studies conducted at subsets of sites. 

Procedures are described that were used for sample analyses, 

quality assurance and quality control, and data management.

The overall goal of the assessment is to improve our understanding of multiple water-quality stressors that affect wadeable streams throughout the region by evaluating relations 

between these stressors and indicators of stream health.

A related study on which the Northeast Stream Quality 

Assessment was built was the Atlantic Highlands flow-ecology 

study conducted during 2014 that investigated 66 streams and 

focused on effects of flow alteration on stream ecosystems. 

The design of the Atlantic Highlands flow-ecology study, 

which consisted of a subset of the many variables considered 

in the 2016 multistressor assessment, is also summarized here.

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Tables 1–2
34 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016 Table 1. Characteristics of stream watersheds in the northeastern United States that were assessed as part of the U.S. Geological Survey Northeast Stream Quality Assessment in 2016. [Latitude and longitude of water-quality-sample locations are based on the North American Datum of 1983 and shown in decimal degrees. Urbanization is represented as a gradient, from tier 1 (least) to tier 5 (greatest). States are abbreviated with two-letter postal codes; for example, NH is New Hampshire. Sites with NWIS station numbers highlighted were also part of the Atlantic Highlands flow-ecology study. U.S. Environmental Protection Agency Level III ecoregions: NCZ, Northeastern Coastal Zone; NEH, Northeastern Highlands; EGLL, Eastern Great Lakes Lowlands; NP, Northern Piedmont; NAP, Northern Allegheny Plateau. Agriculture categories: Ag, agriculture; LowAg, low agriculture; VLowAg, very low agriculture; Ref, reference. NWIS, U.S. Geological Survey National Water Information System; km2, square kilometer] NWIS station number NWIS station name Field identifier Latitude (NWIS) Longitude (NWIS) Ecore- gion Drainage area (km2

)

Urban 

category1

Agriculture 

category2

Site type3

01073319 LAMPREY RIVER AT LANGFORD ROAD, AT RAYMOND, NH NH_Lamprey 43.0414 -71.2017 NCZ 144.4 Tier 1 Ref Light urban01095220 STILLWATER RIVER NEAR STERLING, MA MA_Stillwater 42.4109 -71.7912 NCZ 78.7 Tier 1 Ref Light urban

01096710 ASSABET RIVER AT ALLEN STREET AT NORTHBOROUGH, MA MA_Assabet 42.3294 -71.6300 NCZ 77.9 Tier 3 Ref Urban01097270 FORT POND BROOK AT RIVER ROAD NEAR SOUTH ACTON, 

MA

MA_FortPond 42.4594 -71.4428 NCZ 51.3 Tier 2 Ref Urban

01100600 SHAWSHEEN RIVER NEAR WILMINGTON, MA MA_Shawsheen 42.5681 -71.2148 NCZ 95.9 Tier 5 Ref Urban01101500 IPSWICH RIVER AT SOUTH MIDDLETON, MA MA_Ipswich 42.5695 -71.0270 NCZ 113.7 Tier 4 Ref Urban01102345 SAUGUS RIVER AT SAUGUS IRONWORKS AT SAUGUS, MA MA_Saugus 42.4695 -71.0070 NCZ 64.4 Tier 5 Ref Urban01103280 CHARLES RIVER AT MEDWAY, MA MA_Charles 42.1398 -71.3895 NCZ 169.0 Tier 3 Ref Urban01105000 NEPONSET RIVER AT NORWOOD, MA MA_Neponset 42.1776 -71.2009 NCZ 90.3 Tier 3 Ref Urban01105583 MONATIQUOT RIVER AT EAST BRAINTREE, MA MA_Monatiquot 42.2209 -70.9781 NCZ 74.3 Tier 4 Ref Urban01105600 OLD SWAMP RIVER NEAR SOUTH WEYMOUTH, MA MA_OldSwamp 42.1904 -70.9448 NCZ 12.0 Tier 5 Ref Urban01109000 WADING RIVER NEAR NORTON, MA MA_Wading 41.9476 -71.1767 NCZ 111.7 Tier 3 Ref Urban01109070 SEGREGANSET RIVER NEAR DIGHTON, MA MA_Segreganset 41.8404 -71.1428 NCZ 27.4 Tier 1 Ref Light urban01112262 MILL RIVER AT SUMMER STREET NEAR BLACKSTONE, MA MA_MillSummer 42.0408 -71.5156 NCZ 74.0 Tier 2 Ref Urban01114000 MOSHASSUCK RIVER AT PROVIDENCE, RI RI_Moshassuck 41.8340 -71.4106 NCZ 59.2 Tier 5 Ref Urban01114500 WOONASQUATUCKET RIVER AT CENTERDALE, RI RI_Woonasqua 41.8590 -71.4873 NCZ 97.8 Tier 3 Ref Urban01115110 HUNTINGHOUSE BK AT ELMDALE RD AT N SCITUATE, RI RI_Hunting 41.8468 -71.6117 NCZ 16.1 Tier 1 Ref Light urban01115114 RUSH BROOK NEAR ELMDALE RD NEAR NORTH SCITUATE, 

RI

RI_Rush 41.8376 -71.6120 NCZ 12.2 Tier 1 Ref Light urban

01117800 WOOD RIVER NEAR ARCADIA, RI RI_Wood 41.5740 -71.7206 NCZ 91.2 Tier 1 Ref Light urban01121000 MOUNT HOPE RIVER NEAR WARRENVILLE, CT CT_Hope 41.8437 -72.1690 NCZ 75.1 Tier 1 Ref Light urban01121330 FENTON RIVER AT MANSFIELD, CT CT_Fenton 41.8332 -72.2428 NCZ 49.7 Tier 1 Ref Light urban01123000 LITTLE RIVER NEAR HANOVER, CT CT_LHanover 41.6718 -72.0523 NCZ 77.6 Tier 1 Ref Light urban01154000 SAXTONS RIVER AT SAXTONS RIVER, VT VT_Saxtons 43.1376 -72.4881 NEH 186.7 Ref Ref Forested01154950 COLD RIVER AT HIGH STREET, AT ALSTEAD, NH NH_Cold 43.1494 -72.3617 NEH 193.2 Ref Ref Forested01170100 GREEN RIVER NEAR COLRAIN, MA MA_Green 42.7034 -72.6706 NEH 106.5 Ref Ref Forested
Table 1 35

Table 1. Characteristics of stream watersheds in the northeastern United States that were assessed as part of the U.S. Geological Survey Northeast Stream Quality Assessment in 2016.—Continued[Latitude and longitude of water-quality-sample locations are based on the North American Datum of 1983 and shown in decimal degrees. Urbanization is represented as a gradient, from tier 1 (least) to tier 5 (greatest). States are abbreviated with two-letter postal codes; for example, NH is New Hampshire. Sites with NWIS station numbers highlighted were also part of the Atlantic Highlands flow-ecology study. U.S. Environmental Protection Agency Level III ecoregions: NCZ, Northeastern Coastal Zone; NEH, Northeastern Highlands; EGLL, Eastern Great Lakes Lowlands; NP, Northern Piedmont; NAP, Northern Allegheny Plateau. Agriculture categories: Ag, agriculture; LowAg, low agriculture; VLowAg, very low agriculture; Ref, reference. NWIS, U.S. Geological Survey National Water Information System; km2, square kilometer]

NWIS station 

number NWIS station name Field identifier Latitude (NWIS) Longitude (NWIS) Ecore- gion Drainage area (km2) Urban cat- egory1 Agri- culture category2 Site type3

01174565 WEST BRANCH SWIFT RIVER NEAR SHUTESBURY, MA MA_WBSwift 42.4551 -72.3818 NEH 32.9 Ref Ref Forested

01187300 HUBBARD RIVER NEAR WEST HARTLAND, CT CT_Hubbard 42.0375 -72.9393 NEH 53.5 Ref Ref Forested01189000 PEQUABUCK R AT FORESTVILLE, CT CT_Pequabuck 41.6732 -72.9007 NCZ 118.3 Tier 3 Ref Urban01192500 HOCKANUM RIVER NEAR EAST HARTFORD, CT CT_Hockanum 41.7832 -72.5873 NCZ 190.8 Tier 3 VLowAg Urban01193500 SALMON RIVER NEAR EAST HAMPTON, CT CT_SalmonHam 41.5523 -72.4493 NCZ 260.5 Tier 1 Ref Light urban01194000 EIGHTMILE RIVER AT NORTH PLAIN, CT CT_Eightmile 41.4417 -72.3327 NCZ 52.4 Ref Ref Forested01195490 QUINNIPIAC RIVER AT SOUTHINGTON, CT CT_Quinnipiac 41.6035 -72.8832 NCZ 46.1 Tier 4 Ref Urban01196620 MILL RIVER NEAR HAMDEN, CT CT_MillHamden 41.4204 -72.9027 NCZ 63.6 Tier 2 Ref Urban01199050 SALMON CREEK AT LIME ROCK, CT CT_SalmonLime 41.9423 -73.3910 NEH 76.1 Tier 1 Ref Light urban01203510 POOTATUCK RIVER AT SANDY HOOK, CT CT_Pootatuck 41.4193 -73.2821 NCZ 64.5 Tier 2 Ref Urban01208869 ROOSTER RIVER NEAR FAIRFIELD, CT CT_Rooster 41.1887 -73.2212 NCZ 19.4 Tier 5 Ref Urban01208925 MILL RIVER NEAR FAIRFIELD, CT CT_MillFair 41.1655 -73.2700 NCZ 74.0 Tier 2 Ref Urban01209700 NORWALK RIVER AT SOUTH WILTON, CT CT_Norwalk 41.1638 -73.4195 NCZ 77.5 Tier 1 Ref Light urban01209901 RIPPOWAM RIVER AT STAMFORD, CT CT_Rippowam 41.0661 -73.5493 NCZ 88.6 Tier 2 Ref Urban010965852 BEAVER BROOK AT NORTH PELHAM, NH NH_Beaver 42.7829 -71.3537 NCZ 123.1 Tier 3 Ref Urban01342730 STEELE CREEK AT ILION, NY NY_Steele 43.0066 -75.0417 EGLL 68.0 Ref Ag Agriculture01349150 CANAJOHARIE CREEK NR CANAJOHARIE, NY NY_Canajoharie 42.8761 -74.6031 EGLL 152.8 Tier 1 Ag Agriculture01356190 LISHA KILL NORTHWEST OF NISKAYUNA, NY NY_LishaKill 42.7836 -73.8567 NCZ 41.9 Tier 3 VLowAg Urban01359135 PATROON CREEK AT ALBANY, NY NY_Patroon 42.6634 -73.7462 NCZ 35.7 Tier 5 VLowAg Urban01362200 ESOPUS CREEK AT ALLABEN, NY NY_Esopus 42.1169 -74.3803 NEH 165.0 Ref Ref Forested01362497 LITTLE BEAVERKILL AT BEECHFORD NEAR MT TREMPER, 

NY

NY_LBeaver 42.0194 -74.2664 NEH 43.2 Ref Ref Forested

01372040 CRUM ELBOW CR AT HYDE PARK, NY NY_Crum 41.7906 -73.9302 NCZ 47.0 Tier 1 Ref Light urban01374559 WEST BRANCH CROTON RIVER AT RICHARDSVILLE, NY NY_WBCroton 41.4706 -73.7600 NEH 28.5 Ref Ref Forested01374890 CROSS RIVER NEAR CROSS RIVER, NY NY_Cross 41.2602 -73.6019 NCZ 44.2 Tier 1 Ref Light urban01374930 MUSCOOT RIVER AT BALDWIN PLACE, NY NY_Muscoot 41.3381 -73.7687 NCZ 34.3 Tier 2 Ref Urban01374960 HALLOCKS MILL BROOK AT YORKTOWN HEIGHTS, NY NY_Hallocks 41.2845 -73.7740 NCZ 25.0 Tier 3 Ref Urban
36 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016 Table 1. Characteristics of stream watersheds in the northeastern United States that were assessed as part of the U.S. Geological Survey Northeast Stream Quality Assessment in 2016.—Continued [Latitude and longitude of water-quality-sample locations are based on the North American Datum of 1983 and shown in decimal degrees. Urbanization is represented as a gradient, from tier 1 (least) to tier 5 (greatest). States are abbreviated with two-letter postal codes; for example, NH is New Hampshire. Sites with NWIS station numbers highlighted were also part of the Atlantic Highlands flow-ecology study. U.S. Environmental Protection Agency Level III ecoregions: NCZ, Northeastern Coastal Zone; NEH, Northeastern Highlands; EGLL, Eastern Great Lakes Lowlands; NP, Northern Piedmont; NAP, Northern Allegheny Plateau. Agriculture categories: Ag, agriculture; LowAg, low agriculture; VLowAg, very low agriculture; Ref, reference. NWIS, U.S. Geological Survey National Water Information System; km2, square kilometer] NWIS station number NWIS station name Field identifier Latitude (NWIS) Longitude (NWIS) Ecore- gion Drainage area (km2

)

Urban 

category1

Agriculture 

category2

Site type3

01376500 SAW MILL RIVER AT YONKERS, NY NY_SawMill 40.9364 -73.8861 NCZ 66.1 Tier 4 Ref Urban

01390500 SADDLE RIVER AT RIDGEWOOD, NJ NJ_Saddle 40.9850 -74.0906 NP 54.4 Tier 2 VLowAg Urban01391000 HOHOKUS BROOK AT HO-HO-KUS, NJ NJ_Hohokus 40.9978 -74.1119 NP 43.3 Tier 3 Ref Urban01414500 MILL BROOK NEAR DUNRAVEN, NY NY_MillBrook 42.1061 -74.7306 NEH 65.0 Ref Ref Forested01513550 CHOCONUT CREEK NEAR CHOCONUT, PA PA_Choconut 41.9628 -76.0014 NAP 48.1 Ref VLowAg Forested01513725 NANTICOKE CREEK AT AMES ROAD NEAR MAINE, NY NY_Nanticoke 42.2155 -76.0394 NAP 120.7 Ref LowAg Agriculture01513820 APALACHIN CREEK AT APALACHIN, NY NY_Apalachin 42.0623 -76.1488 NAP 111.4 Ref VLowAg Forested01531250 NB SUGAR CREEK TRIB NEAR COLUMBIA CROSS ROADS, PA PA_NBSugar 41.8404 -76.8269 NAP 23.0 Ref LowAg Agriculture0422026250 NORTHRUP CREEK AT NORTH GREECE, NY NY_Northrup 43.2536 -77.7422 EGLL 26.3 Tier 2 LowAg Urban04229700 SPRING BROOK AT MORAN CORNER, NY NY_Spring 42.9601 -77.6194 EGLL 58.7 Tier 1 Ag Agriculture04232050 ALLEN CREEK NEAR ROCHESTER, NY NY_Allen 43.1303 -77.5186 EGLL 79.7 Tier 3 LowAg Urban04233300 SIXMILE CREEK AT BETHEL GROVE, NY NY_Sixmile 42.4031 -76.4350 NAP 100.1 Ref VLowAg Forested04240105 HARBOR BK AT HIAWATHA BLVD., SYRACUSE, NY NY_Harbor 43.0561 -76.1850 EGLL 31.8 Tier 3 VLowAg Urban04240253 GEDDES BROOK AT FAIRMOUNT, NY NY_Geddes 43.0573 -76.2338 EGLL 21.8 Tier 3 LowAg Urban04245840 SCRIBA CREEK NEAR CONSTANTIA, NY NY_Scriba 43.2597 -76.0028 EGLL 103.0 Ref VLowAg Forested405242073521001 BRONX RIVER AT WOODLAWN CEMETERY AT BRONX, NY NY_Bronx 40.8784 -73.8695 NCZ 138.1 Tier 4 Ref Urban405409073485501 HUTCHINSON RIVER AT COLONIAL AVE AT PELHAM, NY NY_Hutchinson 40.9026 -73.8155 NCZ 18.6 Tier 5 Ref Urban405708073440301 MAMARONECK RIVER AT WARD AVE AT MAMARONECK, NY NY_Mamaroneck 40.9524 -73.7343 NCZ 58.9 Tier 3 Ref Urban411844074085601 RAMAPO RIVER AT RIVER ROAD AT HARRMAN, NY NY_Ramapo 41.3122 -74.1489 NEH 26.6 Tier 3 Ref Urban411959073522901 PEEKSKILL HOLLOW CREEK AT LAKE PEEKSKILL, NY NY_Peekskill 41.3331 -73.8747 NCZ 104.8 Tier 1 Ref Light urban412715074030101 SILVER STREAM AT VAILS GATE, NY NY_Silver 41.4544 -74.0503 NCZ 17.2 Tier 3 LowAg Urban413020074022001 GIDNEYTOWN CREEK AT RT52 AT NEWBURGH, NY NY_Gidneytown 41.5057 -74.0390 NCZ 24.9 Tier 1 VLowAg Light urban413453076041101 LITTLE MEHOOPANY CREEK AT NORTH MEHOOPANY, PA PA_LMehoopany 41.5815 -76.0698 NAP 27.9 Ref Ag Agriculture413735076162701 SUGAR RUN NEAR WILMOT, PA PA_SugarRun 41.6264 -76.2744 NAP 86.9 Ref Ag Agriculture413758073552401 CASPER CREEK AT BRIDGEWATER RD NR WAPPINGERS 

FALLS, NY

NY_Casper 41.6330 -73.9236 NCZ 27.5 Tier 4 Ref Urban

414904073575201 BLACK CREEK ABOVE RTE 9W BRIDGE AT ESOPUS, NY NY_BlackEsopus 41.8181 -73.9645 NCZ 87.3 Tier 1 VLowAg Light urban
Table 1 37

Table 1. Characteristics of stream watersheds in the northeastern United States that were assessed as part of the U.S. Geological Survey Northeast Stream Quality Assessment in 2016.—Continued[Latitude and longitude of water-quality-sample locations are based on the North American Datum of 1983 and shown in decimal degrees. Urbanization is represented as a gradient, from tier 1 (least) to tier 5 (greatest). States are abbreviated with two-letter postal codes; for example, NH is New Hampshire. Sites with NWIS station numbers highlighted were also part of the Atlantic Highlands flow-ecology study. U.S. Environmental Protection Agency Level III ecoregions: NCZ, Northeastern Coastal Zone; NEH, Northeastern Highlands; EGLL, Eastern Great Lakes Lowlands; NP, Northern Piedmont; NAP, Northern Allegheny Plateau. Agriculture categories: Ag, agriculture; LowAg, low agriculture; VLowAg, very low agriculture; Ref, reference. NWIS, U.S. Geological Survey National Water Information System; km2, square kilometer]

NWIS station 

number NWIS station name Field identifier Latitude (NWIS) Longitude (NWIS) Ecore- gion Drainage area (km2) Urban cat- egory1 Agri- culture category2 Site type3

415929076544401 HAMMOND CREEK NEAR WELLS, PA PA_Hammond 41.9963 -76.9074 NAP 75.1 Ref LowAg Agriculture

420103076540701 MUDLICK CREEK AT SEELEY CREEK, NY NY_Mudlick 42.0175 -76.9022 NAP 60.0 Ref Ag Agriculture420722075565001 LITTLE CHOCONUT CR AT ST JOHN’S CH AT JOHNSON CITY, 

NY

NY_LittleChoco 42.1228 -75.9473 NAP 32.7 Tier 2 LowAg Light urban

422223074400201 WEST BRANCH DELAWARE R AT CORNELL AVE BRIDGE, 

HOBART, NY

NY_WBDelaware 42.3731 -74.6673 NAP 41.1 Tier 1 LowAg Light urban

422644076300001 CASCADILLA CREEK AT ITHACA, NY NY_Cascadilla 42.4458 -76.5003 NAP 34.1 Tier 1 LowAg Light urban423533076062101 TROUT BROOK AT CORTLANDVILLE, NY NY_Trout 42.5928 -76.1059 NAP 93.0 Ref LowAg Agriculture423613073422001 MILL CREEK AT EAST GREENBUSH, NY NY_MillGreen 42.6036 -73.7057 NCZ 26.3 Tier 1 Ref Light urban424059073322501 POESTEN KILL AT BLUE FACTORY RD AT BARBERVILLE, NY NY_Poesten 42.6832 -73.5405 NEH 93.0 Ref Ref Forested424143073382901 WYNANTS KILL AT RUSSEL AVE AT WYNANTSKILL, NY NY_Wynants 42.6955 -73.6414 NEH 75.1 Tier 1 VLowAg Light urban424633075300701 SANGERFIELD RIVER AT POOLVILLE, NY NY_Sangerfield 42.7760 -75.5022 NAP 137.0 Ref LowAg Agriculture424643073472901 SHAKERS CREEK AT RIVER ROAD NEAR LATHAM, NY NY_Shakers 42.7787 -73.7915 NCZ 30.0 Tier 4 VLowAg Urban425358073462301 DWAAS KILL SOUTH OF USHERS, NY NY_Dwaas 42.8997 -73.7731 NCZ 45.8 Tier 2 LowAg Urban425540074384801 OTSQUAGO CREEK NEAR FORT PLAIN, NY NY_Otsquago 42.9277 -74.6467 EGLL 155.7 Ref Ag Agriculture430056078044801 BLACK CREEK AT MORGANVILLE, NY NY_BlackMorgan 43.0156 -78.0802 EGLL 56.6 Tier 1 Ag Agriculture430524076084201 LEY CREEK AT LEMOYNE AND FACTORY AT MATTYDALE, NY NY_LeyCreek 43.0901 -76.1451 EGLL 61.7 Tier 5 Ref Urban430557075181801 MUD CREEK AT NEW YORK MILLS, NY NY_MudCreek 43.0992 -75.3050 EGLL 29.1 Tier 2 LowAg Urban430629077274701 THOMAS CREEK AT EAST ROCHESTER, NY NY_Thomas 43.1082 -77.4633 EGLL 76.5 Tier 2 LowAg Urban431542077382401 SLATER CREEK AT HOJACK INDUSTRIAL PARK IN 

ROCHESTER, NY

NY_Slater 43.2617 -77.6400 EGLL 10.7 Tier 5 Ref Urban

1Urban categories represent ranges of percentages of urban land use in a watershed, computed as the total percentages of developed land as defined by the 2006 National Land Cover Database (sum of classes 

22, 23, 24; Fry and others, 2011): Ref, 0–1 percent; tier 1, >1–10 percent; tier 2, >10–20 percent; tier 3, >20–37.5 percent; tier 4, >37.5–50 percent; and tier 5, >50 percent.

2Agriculture categories represent percent row crop land use in a watershed: Ref, 0–1 percent; VlowAg, >1–5 percent; LowAg, >5–15 percent; and Ag, >15 percent.3Site type based on joint designations in the categories of Urban (Urb-cat) and Agriculture (Ag-cat). Forested: Urb-cat = Ref and Ag-cat = Ref or VLowAg; Light Urban: Urb-cat = Tier 1 and Ag-cat = Ref, 

VLowAg, or LowAg; Urban: Urb-cat = Tier 2, 3, 4, or 5 and Ag-cat = Ref, VlowAg, or LowAg; Agriculture: Urb-cat = Ref and Ag-cat = LowAg or Ag, or alternatively Urb-cat = Tier 1 and Ag-cat = Ag.
38 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

Table 2. Summary of data collected at each of the Northeast Stream Quality Assessment sites in 2016.

[Parameters are categorized by the Northeast Stream Quality Assessment study-design components: comprehensive stream water data, focused studies, and 

ecological surveys. Numerical values in the table indicate the number of times samples were collected/analyzed for each parameter type. “I” indicates an integrated sample. “C” indicates a continuous sample. “D” indicates sites where components of ecological surveys were delayed from August until October 2016. 

“1iso” indicates that mercury isotopes were also analyzed. States are abbreviated with two-letter postal codes; for example, NH is New Hampshire. POCIS, 

polar organic chemical integrative sampler; PAH, polycyclic aromatic hydrocarbon; --, not sampled.]

Site information Comprehensive stream water data Focused 

studies Ecological surveys

Field identifier 

Primary 

land-use 

type

Major ions

Nutrients

Pesticides

Glyphosate

Suspended sediment

Dissolved organic carbon

Mercury

Nitrate isotopes

Organic waste indicators

Pharmaceuticals

Algal toxins

POCIS

Stream discharge

Stream stage

Temperature

Pesticide autosampler

Walling tube sediment

Algal productivity

Aquatic biota

Mercury in fish

Sediment chemistry

Sediment PAH

Sediment toxicity

Physical habitat

NH_Lamprey Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 1 -- 1

MA_Stillwater Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1iso 1 1 -- 1

MA_Assabet Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- I -- 1 1 1 1 1 1

MA_FortPond Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 -- 1

MA_Shawsheen Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 2 1 1 1

MA_Ipswich Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- I -- 1 1iso 1 1 1 1

MA_Saugus Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 -- 1 1 1 1

MA_Charles Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C I I -- 1 1iso 2 1 1 1

MA_Neponset Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- I -- 1 1iso 2 1 1 1

MA_Monatiquot Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 2 1 1 1

MA_OldSwamp Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1iso 1 1 1 1

MA_Wading Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 1 1 1 1

MA_Segreganset Light urban 2 2 2 2 2 2 1 1 0 0 0 I C -- C -- -- -- -- -- -- -- -- --

MA_MillSummer Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 1 1

RI_Moshassuck Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C I I -- 1 1 2 1 1 1

RI_Woonasqua Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 1 1 1 1D

RI_Hunting Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 1 1 1

RI_Rush Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 1 -- 1

RI_Wood Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 1 -- 1D

CT_Hope Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 -- -- 1

CT_Fenton Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 1 -- 1

CT_LHanover Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 -- -- 1

VT_Saxtons Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1iso 1 -- -- 1

NH_Cold Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 -- -- 1

MA_Green Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1D 1 1 1 1 1

MA_WBSwift Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1iso 1 -- -- 1

CT_Hubbard Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1iso 1 -- -- 1

CT_Pequabuck Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- C 1D 1 1 1 1 1D

CT_Hockanum Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C I -- -- 1 1 1 1 1 1

CT_SalmonHam Light urban 4 4 4 4 4 4 4 1 3 3 1 I C -- C -- -- C 1 1 1 1 -- 1

CT_Eightmile Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 -- -- 1

CT_Quinnipiac Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1D 1 1 1 1 1D
Table 2 39

Table 2. Summary of data collected at each of the Northeast Stream Quality Assessment sites in 2016.—Continued

[Parameters are categorized by the Northeast Stream Quality Assessment study-design components: comprehensive stream water data, focused studies, and 

ecological surveys. Numerical values in the table indicate the number of times samples were collected/analyzed for each parameter type. “I” indicates an integrated sample. “C” indicates a continuous sample. “D” indicates sites where components of ecological surveys were delayed from August until October 2016. 

“1iso” indicates that mercury isotopes were also analyzed. States are abbreviated with two-letter postal codes; for example, NH is New Hampshire. POCIS, 

polar organic chemical integrative sampler; PAH, polycyclic aromatic hydrocarbon; --, not sampled.]

Site information Comprehensive stream water data Focused 

studies Ecological surveys

Field identifier 

Primary 

land-use 

type

Major ions

Nutrients

Pesticides

Glyphosate

Suspended sediment

Dissolved organic carbon

Mercury

Nitrate isotopes

Organic waste indicators

Pharmaceuticals

Algal toxins

POCIS

Stream discharge

Stream stage

Temperature

Pesticide autosampler

Walling tube sediment

Algal productivity

Aquatic biota

Mercury in fish

Sediment chemistry

Sediment PAH

Sediment toxicity

Physical habitat

CT_MillHamden Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 1 1 -- 1

CT_SalmonLime Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 1 -- 1

CT_Pootatuck Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 1 1 1 1

CT_Rooster Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 2 1 1 1

CT_MillFair Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1iso 1 1 -- 1

CT_Norwalk Light urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- C 1 1 2 1 1 1

CT_Rippowam Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1iso 1 1 1 1

NH_Beaver Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1iso 1 1 1 1

NY_Steele Agriculture 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 1 -- -- 1

NY_Canajoharie Agriculture 9 9 9 9 9 9 4 1 3 3 1 I C -- C I I C 1 1 2 1 1 1

NY_LishaKill Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1D 1D 2D 1D 1D 1D

NY_Patroon Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C I I -- 1D -- 2D 1D 1D 1D

NY_Esopus Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 -- -- 1

NY_LBeaver Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1iso 1 -- -- 1

NY_Crum Light urban 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- -- -- 1 1 1 1 -- 1

NY_WBCroton Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 1 1 1

NY_Cross Light urban 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1iso 1 -- -- 1

NY_Muscoot Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1iso 1 1 1 1

NY_Hallocks Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1iso 1 1 -- 1

NY_SawMill Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1iso 1 1 1 1

NJ_Saddle Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 1 1 1 1

NJ_Hohokus Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 1 1 -- 1

NY_MillBrook Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 -- -- 1

PA_Choconut Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 -- -- 1

NY_Nanticoke Agriculture 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- -- -- 1 1 1 -- -- 1

NY_Apalachin Forested 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- -- -- 1 1 1 -- -- 1

PA_NBSugar Agriculture 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 1 1 1

NY_Northrup Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 1 1 1 1

NY_Spring Agriculture 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 1 1

NY_Allen Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1iso 1 1 1 1

NY_Sixmile Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1 1 -- -- 1

NY_Harbor Urban 9 9 9 9 9 9 4 1 3 3 1 I C -- C -- -- -- 1 1 1 1 1 1
40 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

Table 2. Summary of data collected at each of the Northeast Stream Quality Assessment sites in 2016.—Continued

[Parameters are categorized by the Northeast Stream Quality Assessment study-design components: comprehensive stream water data, focused studies, and 

ecological surveys. Numerical values in the table indicate the number of times samples were collected/analyzed for each parameter type. “I” indicates an integrated sample. “C” indicates a continuous sample. “D” indicates sites where components of ecological surveys were delayed from August until October 2016. 

“1iso” indicates that mercury isotopes were also analyzed. States are abbreviated with two-letter postal codes; for example, NH is New Hampshire. POCIS, 

polar organic chemical integrative sampler; PAH, polycyclic aromatic hydrocarbon; --, not sampled.]

Site information Comprehensive stream water data Focused 

studies Ecological surveys

Field identifier 

Primary 

land-use 

type

Major ions

Nutrients

Pesticides

Glyphosate

Suspended sediment

Dissolved organic carbon

Mercury

Nitrate isotopes

Organic waste indicators

Pharmaceuticals

Algal toxins

POCIS

Stream discharge

Stream stage

Temperature

Pesticide autosampler

Walling tube sediment

Algal productivity

Aquatic biota

Mercury in fish

Sediment chemistry

Sediment PAH

Sediment toxicity

Physical habitat

NY_Geddes Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- I -- 1 1 1 1 1 1

NY_Scriba Forested 4 4 4 4 4 4 3 1 3 3 1 I C -- C -- -- -- 1 1iso 1 1 1 1

NY_Bronx Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C I I -- 1 1iso 2 1 1 1

NY_Hutchinson Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C I -- -- 1 1 2 1 1 1

NY_Mamaroneck Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1iso 1 1 1 1

NY_Ramapo Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 1 1

NY_Peekskill Light urban 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- -- -- 1 1 1 1 -- 1

NY_Silver Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 1 1

NY_Gidneytown Light urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 1 1

PA_LMehoopany Agriculture 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 -- -- 1

PA_SugarRun Agriculture 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 1 1

NY_Casper Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- I -- 1 1iso 1 1 1 1

NY_BlackEsopus Light urban 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- -- -- 1 1 1 -- -- 1

PA_Hammond Agriculture 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- -- -- 1 1 1 -- -- 1

NY_Mudlick Agriculture 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 -- -- 1

NY_LittleChoco Light urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 -- 1

NY_WBDelaware Light urban 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- -- -- 1D 1 1 1 -- 1

NY_Cascadilla Light urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 -- 1

NY_Trout Agriculture 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- -- -- 1 1 1 -- -- 1

NY_MillGreen Light urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- I -- 1D 1D 1D 1D 1D 1D

NY_Poesten Forested 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- I -- 1D 1D 1D -- -- 1D

NY_Wynants Light urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 -- 1

NY_Sangerfield Agriculture 4 4 4 4 4 4 3 1 3 3 1 I -- C C -- -- -- 1 1 1 -- -- 1

NY_Shakers Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 1 1

NY_Dwaas Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1D 1 1 1 1 1

NY_Otsquago Agriculture 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- I C 1 1 1 -- -- 1

NY_BlackMorgan Agriculture 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- I -- 1 1 2 1 1 1

NY_LeyCreek Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1iso 2 1 1 1

NY_MudCreek Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 -- 1

NY_Thomas Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1iso 1 1 1 1

NY_Slater Urban 9 9 9 9 9 9 4 1 3 3 1 I -- C C -- -- -- 1 1 1 1 1 1
Appendixes 1–2

Appendix 1 43

Appendix 1. Description of the Sampling Timelines, 

Matrix, Collection, and Processing for Water, Sediment, and 

Ecological Samples

[Appendix tables are available for download at https://doi.org/10.3133/ofr20181183]

Tables

1.1. Sample matrix for selected sites in the U.S. Geological Survey Northeast Stream

Quality Assessment in 2016

1.2. Onset Computer Corporation specifications for the HOBO Water Temp Pro v2 U22 and 

U20 water level loggers used to monitor continuous water temperature and water 

level, respectively, at selected stream sites as part of the Northeast Stream Quality 

Assessment of the U.S. Geological Survey National Water-Quality Assessment Project 

in 2016

1.3. Description of the data collection and processing steps for water samples collected 

during the U.S. Geological Survey Northeast Stream Quality Assessment study in 2016

1.4. Description of the bottle types, laboratory schedules, preservation, and shipping protocols by parameter group collected by the U.S. Geological Survey Northeast Stream 

Quality Assessment in 2016
44 Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016

Appendix 2. Description of the U.S. Geological Survey 

National Water Quality Laboratory Schedules Used for 

Water, Sediment, and Periphyton

[Appendix tables are available for download at https://doi.org/10.3133/ofr20181183]

Tables

2.1. U.S. Geological Survey National Water Quality Laboratory Schedule 2590 for major 

ions in water

2.2. U.S. Geological Survey National Water Quality Laboratory Schedule 2711 for nutrients 

in water

2.3. U.S. Geological National Water Quality Laboratory Schedule 2437 for current-use 

pesticides in water

2.4. U.S. Geological Survey National Water Quality Laboratory Schedule 2440 for

pharmaceutical compounds in water

2.5. U.S. Geological Survey National Water Quality Laboratory Schedule 4433 for organic 

wastewater indicator compounds in water

2.6. U.S. Geological Survey National Water Quality Laboratory Schedule 5433 for organic 

wastewater indicator compounds in bed sediment

2.7. U.S. Geological Survey National Water Quality Laboratory Schedule 5506 for

semi-volatile organic compounds in bed sediment

2.8. U.S. Geological Survey National Water Quality Laboratory Schedule 8093 for

halogenated organic compounds in bed sediment

2.9. U.S. Geological Survey National Water Quality Laboratory Schedule 6434 for hormone 

compounds in bed sediment

 2.10. U.S. Geological Survey National Water Quality Laboratory Schedule 1632 for

chlorophyll a, pheophytin a, and ash-free dry mass in periphyton
Appendix 2 45

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For more information about this report, contact:

Director, New England Water Science Center

U.S. Geological Survey 

10 Bearfoot Road 

Northborough, MA 01532

dc_nweng@usgs.gov

or visit our website at

https://newengland.water.usgs.gov

Publishing support provided by the Pembroke Publishing 

Service Center
Coles and others—Design and Methods of the U.S. Geological Survey Northeast Stream Quality Assessment (NESQA), 2016—Open-File Report 2018–1183

ISSN 2331-1258 (online)

https://doi.org/10.3133/ofr20181183