National Water-Quality Assessment Program Principal Aquifers

Microbial Quality of the Nation’s Ground-Water 

Resources, 1993–2004

U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2006–5290

NROK

UARK

MARK

ALMN

COOK

OAHU

CHEY

NPLT

SHPL

KNTY

SANJ

SACR NVBR

NVBR

USNK

CCYK

REDN

CAZB RIOG

SCTX

TRIN

CACI

KANS

CNBR

OZRK

UMIS WMIC

LIRB

UIRB LERI

ACAD

MISE

TENN

WHMI

ALBE

ACFB

LSUS

HDSN

DELR

CONN

NECB

LINJ

PUGT

WILL

SOCA

UCOL

SPLT

YELL

EIWA

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KANA

PODL

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SOFL

Microbial Quality of the Nation’s 

Ground-Water Resources, 1993–2004

By S.S. Embrey and D.L. Runkle

National Water-Quality Assessment Program—Principal Aquifers

Scientific Investigations Report 2006–5290

U.S. Department of the Interior

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

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2006

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Although this report is in the public domain, permission must be secured from the individual copyright owners to 

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Suggested citation:

Embrey, S.S., and Runkle, D.L., 2006, Microbial quality of the Nation’s ground-water resources, 1993–2004: U.S. 

Geological Survey Scientific-Investigations Report 2006-5290, 34 p.
iii

Foreword

The U.S. Geological Survey (USGS) is committed to providing the Nation with accurate and timely 

scientific information that helps enhance and protect the overall quality of life and that facilitates 

effective management of water, biological, energy, and mineral resources (http://www.usgs.gov/). 

Information on the quality of the Nation’s water resources is critical to assuring the long-term 

availability of water that is safe for drinking and recreation and suitable for industry, irrigation, and 

habitat for fish and wildlife. Population growth and increasing demands for multiple water uses 

make water availability, now measured in terms of quantity and quality, even more essential to the 

long-term sustainability of our communities and ecosystems.

The USGS implemented the National Water-Quality Assessment (NAWQA) Program in 1991 to 

support national, regional, and local information needs and decisions related to water-quality 

management and policy (http://water.usgs.gov/nawqa). Shaped by and coordinated with 

ongoing efforts of other Federal, State, and local agencies, the NAWQA Program is designed to 

answer: What is the condition of our Nation’s streams and ground water? How are the conditions 

changing over time? How do natural features and human activities affect the quality of streams and 

ground water, and where are those effects most pronounced? By combining information on water 

chemistry, physical characteristics, stream habitat, and aquatic life, the NAWQA Program aims to 

provide science-based insights for current and emerging water issues and priorities. 

From 1991-2001, the NAWQA Program completed interdisciplinary assessments in 51 of the 

Nation’s major river basins and aquifer systems, referred to as Study Units (http://water.usgs.gov/

nawqa/studyu.html). Baseline conditions were established for comparison to future assessments, 

and long-term monitoring was initiated in many of the basins. During the next decade, 42 of the 51 

Study Units will be reassessed so that 10 years of comparable monitoring data will be available to 

determine trends at many of the Nation’s streams and aquifers. The next 10 years of study also will 

fill in critical gaps in characterizing water-quality conditions, enhance understanding of factors that 

affect water quality, and establish links between sources of contaminants, the transport of those 

contaminants through the hydrologic system, and the potential effects of contaminants on humans 

and aquatic ecosystems.

The USGS aims to disseminate credible, timely, and relevant science information to inform 

practical and effective water-resource management and strategies that protect and restore water 

quality. We hope this NAWQA publication will provide you with insights and information to meet 

your needs, and will foster increased citizen awareness and involvement in the protection and 

restoration of our Nation’s waters. 

The USGS recognizes that a national assessment by a single program cannot address all waterresource issues of interest. External coordination at all levels is critical for a fully integrated 

understanding of watersheds and for cost-effective management, regulation, and conservation of 

our Nation’s water resources. The NAWQA Program, therefore, depends on advice and information 

from other agencies—Federal, State, interstate, Tribal, and local—as well as nongovernmental 

organizations, industry, academia, and other stakeholder groups. Your assistance and suggestions 

are greatly appreciated.

 Robert M. Hirsch

Associate Director for Water
iv

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Contents

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

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

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

Purpose and Scope ..............................................................................................................................2

Microbial Indicators of Fecal and Sewage Contamination ...........................................................4

Study Methods ...............................................................................................................................................5

Selection of Wells and Datasets Used in Analyses ........................................................................5

Sample Collection and Measurements.............................................................................................7

Microbial Analyses and Sources of Data.........................................................................................7

Quality Assurance and Quality Control .............................................................................................9

Statistical Analyses............................................................................................................................10

Microbial Quality of Water in Principal Aquifers....................................................................................11

Fecal-Indicator Bacteria and Coliphage Viruses in Study-Unit Well Networks and

Principal Aquifers..................................................................................................................11

Detection of Coliform Bacteria in Principal Aquifers of Different Lithologies..........................19

Water Use, Drinking-Water Supplies, and Wells of the Major Aquifer Study and

Source-Water Quality Assessment Networks .................................................................21

Coliphage Viruses and Water Supplies...........................................................................................24

Occurrence of Coliform Bacteria and Relation to Well Depth and Selected

Water-Quality Characteristics.............................................................................................24

Discussion.....................................................................................................................................................29

Summary........................................................................................................................................................31

Acknowledgments.......................................................................................................................................32

References Cited..........................................................................................................................................32
vi

Figures

Figure 1. Map showing study units of the National Water-Quality Assessment program

in which microbiological samples were collected from wells, 1993–2004............ 2

Figure 2. Graph showing numbers of test results for fecal-indicator microorganisms 

by each analytical method for environmental and quality-control samples

collected from wells in 22 study units of the National Water-Quality

Assessment program, 1993–2004 ......................................................... 8

Figure 3. Maps showing locations of wells in principal aquifers that tested positive for

fecal-indicator bacteria and wells where fecal-indicator bacteria were not

detected in samples collected for the National Water-Quality Assessment

program, 1993–2004 ........................................................................ 12

Figure 4. Graph showing number of wells sampled and number of wells with

detections of coliform bacteria in samples collected in 22 study units of the

National Water-Quality Assessment program, 1993–2004.............................. 13

Figure 5. Graphs showing percentage of wells testing positive for total coliform

bacteria and Escherichia coli, and concentrations of coliform bacteria by

study network in samples collected in 22 study units of the National

Water-Quality Assessment program, 1993–2004 ....................................... 14

Figure 6. Graphs showing percentage of wells testing positive for coliform bacteria, 

and significantly different (p-value <0.0006) detection frequencies of total

coliform bacteria by principal aquifer from data collected in 22 study units of

the National Water-Quality Assessment program, 1993–2004 ........................ 15

Figure 7. Graphs showing percentage of detections of coliform bacteria and coliphage

virus in wells sampled as part of the major aquifer studies and source-water

quality assessments for the National Water-Quality Assessment program,

1993–2004 .................................................................................... 17

Figure 8. Boxplot showing concentrations of total coliform and Escherichia coli by

principal aquifer in samples collected in 22 study units of the National

Water-Quality Assessment program, 1993–2004 ....................................... 18

Figure 9. Graphs showing percentage of wells testing positive for coliform bacteria,

and significantly different detection frequencies (p-value <0.002) of total

coliform bacteria with respect to aquifer lithology .................................... 19

Figure 10. Boxplot showing concentrations of total coliform and Escherichia coli by

principal aquifer lithology in samples collected in 22 study units of the

National Water-Quality Assessment program, 1993–2004.............................. 20

Figure 11. Graph showing percentage of major aquifer study (MAS) and source-water

quality assessment (SWQA) wells sampled by class of water use in 22 study

units of the National Water-Quality Assessment program, 1993-2004 ............... 21

Figure 12. Graph and boxplot showing percentage of wells testing positive for coliform

bacteria, and concentrations of coliform bacteria by class of water use in

samples collected in major aquifer study (MAS) and source-water quality

assessment (SWQA) wells in 22 study units of the National Water-Quality

Assessment program, 1993–2004 ......................................................... 23

Figure 13. Graphs showing relation of the presence or absence of coliphage virus to

concentrations of total coliforms for wells in the major aquifer study (MAS)

networks and source-water quality assessment (SWQA) networks, and for

principal aquifers with coliphage-positive wells ....................................... 25
vii

Figure 14. Boxplot showing distributions of well depths for the major aquifer study

(MAS), land use study (LUS), and source-water quality assessment (SWQA)

networks, and distribution of well depths for the classes of water use, from

data collected in 22 study units of the National Water-Quality Assessment

program, 1993–2004 ........................................................................ 26

Figure 15. Boxplot showing distribution of well depths in the 16 principal aquifers

studied by the National Water-Quality Assessment program, 1993–2004 ............ 27

Figure 16. Scatterplot showing total-coliform concentrations and depths of wells for all

16 principal aquifers combined on the basis of the median depths of sampled

wells, from data collected in 22 study units of the National Water-Quality

Assessment program, 1993–2004 ......................................................... 28

Figure 17. Boxplots showing detections of total-coliform bacteria with concentrations

of dissolved oxygen, nitrite-plus-nitrate nitrogen, and orthophosphate in

samples collected from wells in 22 study units of the National Water-Quality

Assessment program, 1993–2004 ......................................................... 29

Figures—Continued

Tables

Table 1. Total estimated withdrawals of water from selected principal aquifers and

withdrawals used for public supplies, irrigation, and self-supplied industrial

in the United States, 2000 .................................................................. 3

Table 2. Principal aquifers, primary lithology of the aquifers, well-sampling networks

within each study unit, and the total number of wells sampled during water

years 1993–2004.............................................................................. 6

Table 3. Consolidations and adjustments to the raw microbiological and associated

ground-water data by study unit and network, water use, principal aquifer,

and lithology ................................................................................. 9

Table 4. Summary of microbiological data collected from wells in major aquifer study,

land-use study, and source-water quality assessment networks in 22 study

units of the National Water-Quality Assessment Program, 1993–2004 ............... 13

Table 5. Summary of microbiological data collected from wells in each principal

aquifer in 22 study units of the National Water-Quality Assessment Program,

1993–2004 .................................................................................... 16

Table 6. Summary of microbiological data, by type of principal-aquifer lithology,

collected from wells in 22 study units of the National Water-Quality

Assessment program, 1993–2004 ......................................................... 20

Table 7. Summary of microbiological data collected from major aquifer study and

source-water-quality assessment wells used for domestic, public supply, and

other purposes, and from unused wells by the National Water-Quality

Assessment Program, 1993–2004 ......................................................... 22

Table 8. Summary of coliphage data collected from major aquifer study and

source-water quality assessment wells in each principal aquifer studied by

the National Water-Quality Assessment program, 1993–2004 ........................ 24
viii

Conversion Factors and Abbreviations, Acronyms, and 

Symbols 

Conversion Factors

Multiply By To obtain

cubic foot (ft3) 0.02832 cubic meter

foot (ft) 0.3048 meter

gallon (gal) 3.785 liter

gallon per minute (gal/min) 0.06309 liter per second

gallon per day (gal/d) 0.003785 cubic meter per day

inch of mercury at 60oF (in Hg) 3.377 kilopascal

mile (mi) 1.609 kilometer

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

ounce, fluid (fl. Oz) 0.02957 liter

ounce, avoirdupois (oz) 28.35 gram

pound, avoirdupois (lb) 0.4536 kilogram

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

°F=(1.8×°C)+32

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

°C=(°F-32)/1.8

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 in milligrams per liter (mg/L) or 

micrograms per liter (μg/L).

Concentrations of microorganisms in water are given in colony forming units per 100 milliliters 

(CFU/100mL).
ix

Conversion Factors and Abbreviations, Acronyms, and 

Symbols—Continued

Abbreviation, 

Acronym, or Symbol Meaning

ACFB Alplachicola-Chattahoochee-Flint study unit

ALBE Albemarle-Pamlico study unit

APHA American Public Health Association

CCYK Central Columbia Plateau–Yakima study unit

E. coli Escherichia coli

GAFL Georgia-Florida study unit

HPGW High Plains Ground Water study unit

KANA Kanawha study unit

LERI Lake Erie study unit

LSUS Lower Susquehanna study unit

LUS land-use studies

MAS major-aquifer studies

NAWQA National Water-Quality Assessment Program

NFM National Field Manual

NWIS National Water Information Services

OWML Ohio Water Microbiological Laboratory

OZRK Ozark Plateaus study unit

PODL Potomac-Delmarva study unit

PUGT Puget Sound Basin study unit

QA quality assurance

QC quality control

REDN Red River of the North study unit

SANJ San Joaquin study unit

SANT Santee study unit

SPLT South Platte study unit

SWQA source-water quality assessments

TENN lower and upper Tennessee study unit

TRIN Trinity study unit

UCOL Upper Colorado study unit

USEPA U.S. Environmental Protection Agency

USGS U.S. Geological Survey

USNK Upper Snake study unit

< less than

> greater than
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Abstract

As part of the National Water-Quality Assessment 

(NAWQA) program, microbiological data were collected 

from wells in 22 NAWQA study units during 1993–2004. 

The wells constituted the sampling networks for three major 

NAWQA efforts—the major aquifer study, the land-use study, 

and source-water quality assessments of ground water used for 

public supplies. Sixteen principal aquifers were represented by 

these well networks. Samples of untreated ground water were 

analyzed for concentrations of fecal-indicator bacteria, which 

included the total-coliform bacteria, fecal-coliform bacteria, 

and Escherichia coli, and for the presence of somatic and 

male-specific coliphage viruses.

Analyses of the samples showed that coliform bacteria 

occur relatively frequently—nearly 30 percent of all wells 

tested positive—and that domestic wells commonly are 

contaminated by total coliform bacteria, with 33 percent of 

these wells testing positive. Coliphage viruses were present 

in 10 percent or fewer of the wells sampled in the Central 

Columbia Plateau-Yakima, Georgia-Florida, San Joaquin, and 

Trinity study units, which represent the Columbia Plateau, 

Floridan, Central Valley, and Coastal Lowlands principal 

aquifers, respectively. The frequency of detections and 

concentrations of total coliform bacteria generally were higher 

in samples from domestic wells than in samples from publicsupply wells; in fractured or porous rock materials (carbonate 

rocks) than in unconsolidated materials (mixtures of sand, 

gravel, clay); and in principal aquifers with median depths of 

sampled wells ranging from 100 to 200 feet than in principal 

aquifers with median depths of sampled wells less than 

100 feet or greater than 200 feet.

The waters most affected by the presence of coliform 

bacteria were those in the Valley and Ridge, the Floridan, 

and the Piedmont and Blue Ridge aquifers, where more than 

50 percent of the study wells tested positive for these bacteria. 

The numbers of wells with detections of coliform bacteria 

were significantly lower for the Glacial Deposits, Stream 

and River Valley, Columbia Plateau, Basin and Range, High 

Plains, Southeastern Coastal Plain, and Coastal Lowlands 

aquifers. Of the 16 principal aquifers sampled, wells in the 

Valley and Ridge had the highest overall concentrations of 

total coliforms, with a median of 2 colony-forming units per 

100 milliliters. Elevated concentrations of coliform bacteria 

(greater than 300 colony-forming units per 100 milliliters) 

also were reported for wells completed in the MississippianPennsylvanian aquifer and the Ordovician aquifer in lower 

Tennessee.

More than 50 percent of wells completed in carbonate 

or crystalline rocks tested positive for coliform bacteria. 

The Floridan, Piedmont and Blue Ridge, Ordovician (lower 

Tennessee), and Valley and Ridge aquifers are composed of 

these types of rocks. The lowest detection frequencies (less 

than 5 percent) were for wells in the Basin and Range and 

the Snake River aquifers. The materials that constitute these 

aquifers primarily are unconsolidated sand, gravel, and clay, or 

basalt with interbeds of sand, gravel, or clay.

No strong correlations between concentrations of total 

coliforms and well depths were identified, nor were there 

any correlations between total coliform concentrations 

and selected chemical constituents in the waters. Other 

factors, such as geohydrologic characteristics, proximity of 

contaminating sources, interactions with surface water, or 

well-construction features (including the age of the well), 

likely control the presence and transport of coliform bacteria 

in the ground water.

Introduction

In 1991, the U.S. Geological Survey (USGS) began the 

National Water-Quality Assessment (NAWQA) program to 

study the quality of the Nation’s surface- and ground-water 

resources in more than 50 major river basins and aquifers. 

During the first 10 years of study (Cycle I), the primary goals 

of the program were to assess the water-quality conditions of 

the Nation’s streams and ground water, the effects of human 

activities and natural features on the quality of water, and 

changes in the quality over time (Gilliom and others, 2001). 

In 2001, at the beginning of the program’s second 10-year 

cycle (Cycle II) of intensive studies, NAWQA investigators 

returned to 14 major river-basin and aquifer systems (Gilliom 

and others, 2001). The second set of Cycle II studies of 14 

systems began in 2004, and studies of a third set of 14 systems 

will begin in 2007, bringing the total to 42 of the Nation’s 

most important river-basin and aquifer systems (Gilliom and 

Microbial Quality of the Nation’s Ground-Water 

Resources, 1993–2004

S.S. Embrey and D.L. Runkle
others, 2001). Cycle II emphasizes building upon the initial 

assessments of water quality and studying in detail the longterm trends and the factors that affect water quality (Gilliom 

and others, 2001). NAWQA’s Cycle II ground-water studies 

focus on regional assessments to evaluate water-quality 

conditions and trends in 16 or more principal aquifers, most of 

which underlie several states (Lapham and others, 2005).

NAWQA study units generally are defined by the 

boundaries of major-river basins and aquifer systems. Within 

each study unit, well networks were established to study the 

ground-water resources. In some cases, study units extended 

data collection outside of original geographic delineations 

to meet particular study unit, local, or national objectives. A 

group of network wells typically is sampled once during each 

10-year cycle; however, the sampling frequency can vary 

among the study units.

Fecal and sewage contamination of water can introduce 

pathogenic microorganisms, including bacteria and viruses, 

into a water resource (Geldreich, 1966). Data obtained from 

the collection of water samples from wells and analyzed for 

the presence of fecal-indicator microorganisms can be used 

in multiple ways. Perhaps most importantly, data indicating 

the presence or absence of fecal-indicator microorganisms 

in ground-water samples can help determine the suitability 

of a water resource for different purposes, particularly as 

a drinking-water resource. The collection of ground-water 

samples for the NAWQA program and the analyses for the 

occurrence of fecal-indicator bacteria and fecal-indicator 

viruses contributed to the discussion of the microbial quality 

of ground water in regions across the United States.

Purpose and Scope

This report summarizes microbiological data collected 

from wells by the NAWQA program from 1993 through 

2004. The report describes (1) the occurrence and distribution 

of fecal-indicator bacteria and viruses in principal aquifers, 

and (2) the quality of water used for drinking-water supplies 

in the United States. All microbiological data collected in 

27 NAWQA study units during Cycle I and several Cycle II 

studies (fig. 1) were inventoried for this analysis. However, 

Figure 1. Study units of the National Water-Quality Assessment program in which microbiological samples were collected 

from wells, 1993–2004. (See table 2 for explanation of study-unit name abbreviations.)

NROK

UARK

MARK

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COOK

OAHU

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No microbiological samples

Discontinued study units with no microbiological samples

Microbiological samples collected

EXPLANATION

HPGW, High Plains Ground Water study area

SANJ

SACR NVBR

NVBR

USNK

CCYK

REDN

CAZB RIOG

SCTX

TRIN

CACI

KANS

CNBR

OZRK

UMIS WMIC

LIRB

UIRB LERI

ACAD

MISE

TENN

WHMI

ALBE

ACFB

LSUS

HDSN

DELR

CONN

NECB

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   Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
Table 1. Total estimated withdrawals of water from selected principal aquifers and 

withdrawals used for public supplies, irrigation, and self-supplied industrial in the United 

States, 2000.

[From Maupin and Barber, 2005. Abbreviations: Mgal/d, million gallons per day]

Principal aquifers and 

aquifer systems

Withdrawals (Mgal/d)

Total Public supplies Irrigation Industrial

Columbia Plateau 1,076 223 810 43

Snake River Plain 3,075 151 2,899 25

Floridan 3,640 1,330 1,930 385

Piedmont-and-Blue Ridge 175 110 30 35

Basin-and-Range 5,696 1,081 4,550 65

Central Valley 9,808 839 8,910 59

Glacial Deposits 3,553 1,950 1,020 583

High Plains 17,488 389 17,000 99

Coastal Lowlands 2,368 1,010 933 425

Mississippi Embayment-Texas 

Coastal Uplands

1,327 724 383 220

North Atlantic Coastal Plain 1,035 793 70 172

Ordovician 5.8 4.8 .6 .4

Valley-and-Ridge 362 226 6.3 129

Mississippian-Pennsylvanian 418 289 12 117

Southeastern Coastal Plain 860 340 382 138

Stream-and-River Valley 1,800 456 1,190 154

Denver Basin 36 17 12 7.4

Ozark Plateaus 165 131 20 14

for describing the microbial quality of the ground-water 

resources of geographic regions and the principal aquifers, this 

assessment was limited to that of 22 Cycle I and Cycle II study 

units for which data sets consisted of information from at least 

15 wells.

The wells sampled by these study units make up large 

networks designated as major-aquifer studies (MAS); landuse studies (LUS), including the focused land-use studies 

in agricultural and urban regions; and source-water quality 

assessments (SWQA) of ground water used for public 

supplies. A smaller network consists of reference wells, 

which are primarily for monitoring background water quality. 

Because only two reference-network wells in this data set 

were sampled for fecal-indicator bacteria, that network was 

not included in this analysis. The large networks included 

wells that represented 16 of the 62 principal aquifers and 

aquifer systems described by the USGS Office of Ground 

Water in The National Atlas of the United States of America 

(U.S. Geological Survey, 2003). Total withdrawals from the 

16 principal aquifers used for irrigation, public supply, and 

industrial purposes amounted to about 53,000 Mgal/d (Maupin 

and Barber, 2005). Seventy-six percent of these withdrawals 

were for irrigation purposes and 19 percent for public supplies. 

The water withdrawn from the High Plains principal aquifer in 

2000 amounted to 17,500 Mgal/d (Maupin and Barber, 2005), 

the greatest amount of the 16 principal aquifers (table 1). The 

Central Valley, Calif., principal aquifer supplied the second 

highest amount of water (9,800 Mgal/d) (Maupin and Barber, 

2005), which was used mostly for irrigation.

Introduction   
Microbial Indicators of Fecal and Sewage 

Contamination

Direct analysis of pathogens in water is difficult 

and impractical (IAWPRC Study Group, 1991; Havelaar 

and others, 1993), but certain readily cultured bacteria, 

particularly the coliform and fecal streptococcus groups and 

bacteriophages (viral pathogens of bacteria), can be used 

as indicators of contamination. The total-coliform group is 

a broad group with several members of fecal and nonfecal 

origin. Over time, microbiologists have developed methods 

for analysis and enumeration of bacteria (Geldreich, 1966), 

such as the coliform species Escherichia coli (E. coli) and 

enterococci, that are specific for fecal contamination of water 

because they are consistently and nearly exclusively found 

in feces of warm-blooded animals (Cabelli, 1978; Gerba, 

1987). The fecal-coliform group is a heat-tolerant subset 

of the total-coliform group and is differentiated in part by 

incubation at body temperature (44.5°C) rather than at 35°C, 

the temperature used to culture total coliforms. The fecalcoliform group is intermediate to the total coliforms and E. 

coli with respect to functioning as a fecal indicator because 

the test recovers species of nonfecal origin as well as E. 

coli and other fecal-origin coliforms. However, because the 

major species of the fecal-coliform group is E. coli (U.S. 

Environmental Protection Agency, 1978), the group has been 

extensively used for indicating fecal contamination (Geldreich, 

1966). Some NAWQA studies included analyses for the fecalcoliform group, either in conjunction with, or in place of, the 

total coliforms.

The presence, or absence, of the total-coliform group 

has long been used for assessing drinking-water quality and 

has been written into water-quality standards promulgated as 

early as 1914 by the Public Health Service (McKee and Wolf, 

1963). The coliform group, as defined by the American Public 

Health Association (APHA), is the principal indicator of the 

suitability of a water resource for domestic household or other 

uses. Although differentiation of the members of the coliform 

group, such as the fecal coliforms or E. coli, can be useful 

for evaluating a water resource for special study purposes, 

such as possible sources and types of contamination or how 

recent the contamination, the APHA considers the presence 

of any coliform bacteria in drinking water as unsatisfactory 

(American Public Health Association, 1998).

The U.S. Environmental Protection Agency (USEPA) 

regulates public drinking-water supplies through the Safe 

Drinking Water Act of 1974 (U.S. Environmental Protection 

Agency, 2003). USEPA’s Total Coliform Rule of 1989 

established maximum contaminant levels for total coliform 

bacteria, including fecal coliforms and E. coli, in publicsupply distribution systems and specified routine sampling 

requirements (U.S. Environmental Protection Agency, 2001a). 

The Total Coliform Rule also requires that if a sample of the 

finished (treated) water tests positive for total coliforms, the 

positive sample is tested for the presence of fecal coliforms 

or E. coli. The Ground Water Rule (U.S. Environmental 

Protection Agency, 2006) requires among other activities, 

disinfection of ground water “as necessary,” sanitary surveys, 

and source-water monitoring.

The USEPA does not regulate the quality of water from 

privately owned, domestic wells used for drinking water. 

However, the agency provides a web site (http://www.epa.

gov/safewater/privatewells/index2.html) at which private 

well owners can access an array of basic information and 

guidance on protecting their well water from contamination. 

USEPA also participates in a partnership of a number of 

other organizations, including Farm*A*Syst/Home*A*Syst, 

American Ground Water Trust, and the National Ground Water 

Association, that provide technical assistance and information 

for well owners.

Clostridium perfringens (C. perfringens) is a noncoliform 

species of bacteria that forms resistant spores that enhance 

survival of the organism outside of its normal habitat. The 

spores are resistant to sewage treatment processes and 

disinfection that readily kill members of the coliform group. 

C. perfringens is a useful fecal indicator in tropical climates 

and for tracking point sources of wastewater. The organism 

has been proposed as a surrogate for other spore-forming 

microorganisms such as Cryptosporidium that the traditional 

coliform groups might not adequately represent (Bisson and 

Cabelli, 1980)

Microorganisms of fecal origin are affected differently 

on entering the aquatic environment (Bisson and Cabelli, 

1980; Havelaar and others, 1993), and no single indicator 

can address all concerns about the sanitary quality of the 

water (Cabelli, 1978). For ground water, enteric viruses 

are of particular concern because they are thought to be 

responsible for many infectious gastrointestinal illnesses 

related to the consumption of ground water (Borchardt and 

others, 2004). The U.S. Centers for Disease Control reported 

that during 2001–02, 23 of 25 non-Legionella outbreaks (92 

percent) of drinking-water illnesses were linked to groundwater sources, and 5 of the 25 outbreaks (20 percent) were 

attributed to viruses (norovirus) (Blackburn and others, 

2004). Bacteria, partly because of different survival rates, 

might be inappropriate for indicating the presence of viruses 

in water (Metcalf, 1978; Palmateer and others, 1991; 

   Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
Havelaar and others, 1993). Therefore, some researchers 

have suggested using the coliphage viruses (referred to as 

coliphage), particularly the male-specific coliphage (Gerba, 

1987; Havelaar and others, 1993), and other bacteriophages 

as indicators of the potential presence of enteric viruses 

(DeBartolomeis and Cabelli, 1991; Havelaar and others, 1993; 

Sobsey and others, 1995).

The specific interest in the male-specific coliphage is 

their resemblance to human enteric viruses in morphology, 

genetic material, and similar resistance to environmental 

stresses and disinfection processes (Bitton, 1980; Sobsey and 

others, 1995). Coliphage infect cells of E. coli by attaching 

directly to the outer cell membrane (somatic coliphages) or to 

the F pilus of E. coli cells that contain the F plasmid (malespecific or F-specific coliphages) (International Association 

on Water Pollution Research and Control Study Group, 1991). 

Some organisms, such as the coliphages, appear to be specific 

indicators for sewage because they are consistently isolated 

in large, but variable numbers from sewage, and infrequently 

isolated or isolated only in low numbers from the feces of 

healthy individuals (Cabelli, 1978; Gerba, 1987; International 

Association on Water Pollution Research and Control Study 

Group, 1991). Studies conducted to show relations between 

the presence of enteric viruses with the presence of coliphage 

or the fecal-indicator bacteria in ground water supplies have 

reported mixed results (Francy and others, 2004). Some 

studies have shown a poor relation between the occurrence 

of enteric viruses and coliphage or with the fecal-indicator 

bacteria (Borchardt and others, 2003; Borchardt and others, 

2004; Francy and others, 2004), and others have shown 

significant positive correlation between infectious total virus 

and the coliphage or total coliforms, E. coli, or enterococcus 

(Francy and others, 2004). Thus, the detection of coliphages 

in the NAWQA well samples does not indicate that pathogenic 

viruses also will be detected in the water; rather, the coliphage 

detection is more an indication of the potential for the 

transport of other viruses into the subsurface.

Study Methods

This section describes the establishment of the NAWQA 

study networks and the procedures used to select existing 

wells or construct new wells that were sampled for chemical 

and microbial quality. Procedures for the collection and 

handling of the ground-water samples, as well as the different 

microbiological analytical techniques used during the first 

and second cycles of the NAWQA program are described. 

Other parts of the section discuss quality assurance and 

quality-control procedures used for microbial-sample analyses 

and the statistics that were applied in the summaries of the 

microbiological data.

Selection of Wells and Datasets Used in 

Analyses

The selection or installation of wells for study networks 

followed NAWQA protocols that guide choosing site locations 

relative to land use, describe the suitability of existing wells 

with respect to plumbing and type of pump, and detail the 

construction of new monitoring wells regarding materials and 

drilling methods to meet the program’s study objectives (Scott, 

1990; Koterba and others, 1995; Lapham and others, 1995). 

Selection of wells for the SWQA networks followed NAWQA 

guidelines described by Gregory Delzer (U.S. Geological 

Survey, written commun., June 2002, rev. March 2003).

The water from these wells is used for various purposes, 

including irrigation, stock watering, and recreation, as well 

as domestic and public drinking-water supply. Water use 

is designated as “unused” or “test” for wells used only for 

monitoring purposes such as water-level or water-quality 

measurements.

Within 27 study units, samples were collected from 

1,244 wells in 16 principal aquifers of the United States. 

Through combinations of well networks (MAS, LUS, SWQA), 

most study units sampled more than 20 wells; however, the 

numbers sampled ranged from 2 wells in the Red River of 

the North (REDN) to 155 in the Lower Susquehanna (LSUS) 

(table 2). From the 1,244 wells, 1,784 samples (including 

replicate samples for quality control) were analyzed for 

concentrations of fecal-indicator bacteria and the presence 

or absence of coliphages. Field measurements of water 

temperature, pH, specific conductance, and concentrations of 

dissolved oxygen were taken at the time of sample collection. 

Water samples were analyzed for a broad range of constituents 

including nutrients, major ions, trace elements, and pesticides.

For describing the microbial quality of the Nation’s 

ground-water resources, 15 wells in each study unit were 

considered to be the minimum for representing or describing 

the quality of the ground water of a region or a principal 

aquifer. Therefore, data for individual study units that sampled 

less than 15 wells total from all their networks were removed 

from this analysis. This criterion reduced the number of study 

units from 27 to 22 and the number of wells sampled from 

1,244 to 1,205. The five study units removed from the data set 

were Apalachicola-Chattahoochee-Flint (ACFB), AlbemarlePamlico (ALBE), Ozark Plateaus (OZRK), Red River of the 

North (REDN), and South Platte (SPLT) (table 2).

Study Methods 
Principal aquifers Primary lithology Study unit Study networks Number of 

wells sampled

Data collection years 

(water year)

Columbia Plateau Volcanic (basalt sand and gravel 

interbeds) CCYK MAS-1b, SWQA 44 2002, 2003

Snake River Plain Volcanic (basalt sand and gravel 

interbeds) USNK MAS-1, MAS-2, LUSCR-1 82 1993, 1994, 1996

Floridan Limestone GAFL MAS-2, SWQA-1, SWQA-2 60 2002, 2003

ACFB1 SUS-11 19 2002, 2003

Piedmont and Blue Ridge

Crystalline rocks 

(metamorphic, schist, granite)

ACFB1 LUSUR-11 11 1994

KANA MAS-2 30 1997

PODL SWQA-1 15 2003

LSUS MAS-2 30 1994

Carbonate rocks 

(limestone, dolomite) LSUS LUSAG-1 30 1993

Basin and Range

Sand, gravel, clay

NVBR

MAS-2, SWQA-1, LUSUR-2 41 2003

Limestone MAS-4 18

Volcanic (basalt sand and gravel 

interbeds)

MAS-2 4

Central Valley Sand, gravel, silt SANJ MAS-1, MASCR-1a 30 2002

Alluvium SWQA-1 15 2003

Glacial Deposits Sand, gravel, clay

CONN MAS-2, SWQA-1 45 2002, 2003

DELR MAS-3 16 2001

HPGW SWQA-1 15 2003

LERI LUSspecial-1 28 1997

PUGT LUSCR-1, LUSRS-1, FPSCR-1 27 1998

WHMI SWQA 15 2003

WMIC MAS-2 28 2003

REDN1 LUSAG1 12 2000

High Plains Sand, gravel HPGW MAS-4, MAS-5 57 2003, 2004

Coastal Lowlands Sand, semiconsolidated sand TRIN MAS-3, SWQA-1 45 2002, 2003

Mississippi EmbaymentTexas Coastal Uplands Semiconsolidated sand ACAD MAS-3 21 2004

North Atlantic Coastal Plain

Sand, clay, semiconsolidated 

sand PODL MAS-1, MAS-2, LUSspecial-1 50 2001, 2002, 2003, 2004

Limestone1 ALBE1 SUS-71 19 2002, 2003

Ordovician Limestone TENN 

(lower)

MAS-2 30 2000, 2001

Valley and Ridge

Shale, sandstone DELR MAS-2 30 2000

LSUS MAS-1 29 1993

Limestone, dolomite

LSUS LUSAG-2, LUSAG-3, LUSUR-1 66 1994, 1995

TENN 

(upper)

MAS-1 30 1999

Mississippian-Pennsylvanian

Sedimentary KANA LUSMI-1, MAS-1 57 1997, 1998

Carbonate rocks (residuum, 

limestone, dolomite)

TENN 

(lower)

MAS-1, LUSAG-1 64 1999, 2000, 2001

Southeastern Coastal Plain Sand, clay MOBL LUSRC-1 30 2000

SANT MAS-1 28 1997

Stream and River Valley Alluvium UCOL

MAS-1, MAS-2, LUSRC-1a, 

LUSRC-1b, LUS-1c, LUS-1d, 

LUS-1e

68 1997, 1998

YELL LUSother-1 28 2001

Denver Basin1 Shale, sandstone1 SPLT1 SWQA-11 112 2003

Ozark Plateaus1 Limestone1 OZRK1 LUSAG-2a1, REF-11 16 2002

1

 Study unit, well-sampling network, and wells not included in final analyses of this report.

Table 2. Principal aquifers, primary lithology of the aquifers, well-sampling networks within each study unit, and the total number of 

wells sampled during water years 1993–2004.

[Study unit: ACAD, Acadian; ACFB, Apalachicola-Chattahoochee-Flint; ALBE, Albemarle-Pamlico; CCYK, Central Columbia Plateau-Yakima; CONN, 

Connecticut; DELR, Delaware; GAFL, Georgia-Florida; HPGW, High Plains; KANA, Kanawha; LERI, Lake Erie; LSUS, Lower Susquehanna; MOBL, Mobile; 

NVBR, Nevada basin and range; OZRK, Ozark Plateaus; PODL, Potomac-DelMarva; PUGT, Puget Sound basin; REDN, Red River of the North; SANJ, San 

Joaquin; SANT, Santee; SPLT, South Platte; TENN, lower and upper Tennessee; TRIN, Trinity; UCOL, upper Colorado; USNK, Upper Snake River; WHMI, 

White-Miami; WMIC, Western Lake Michigan; YELL, Yellowstone. Study networks: MAS, major aquifer study; SUS, study unit survey (during Cycle I; 

equivalent to Cycle II MAS); SWQA, source-water quality assessment; LUS, land-use study; CR, cropland; AG, agriculture; UR, urban; RS, residential; RC, 

new residential/commercial; MI, mining; REF, reference; FPS, flow-path study. Lower case letters and numbers following study network indicate study unit or 

NAWQA network coding]

 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
Sample Collection and Measurements

The collection, handling and processing, and laboratory 

analyses of the samples, and field measurements made during 

their collection, followed USGS protocols and the guidelines 

of the NAWQA program during the early years of Cycle I 

(Koterba and others, 1995). The USGS National Field Manual 

(NFM), which in the late 1990s consolidated numerous 

guidance documents, technical memoranda, and sampling 

protocols, became the primary guide for the collection of 

water-quality data in the USGS. Chapters A1-A6 of the 

NFM guide the selection and cleaning of equipment, the 

collection and processing of water samples, and methods of 

measurements performed in the field (U.S. Geological Survey, 

variously dated); chapter A7 specifically guides the collection 

and processing of water for biological indicators (Myers and 

Wilde, 2003).

All equipment used in the collection and processing of 

water samples for microbiological analyses was thoroughly 

cleaned with laboratory-grade detergent followed by several 

rinses with deionized or reagent-grade water. Following the 

cleaning, all equipment for microbiological sampling and 

processing was sterilized before use by means of steam heat 

and pressure (autoclaving) or chemical disinfection (bleach or 

alcohol). Exceptions to autoclaving or chemical disinfection 

might apply to the submersible pumps used to collect water 

from monitoring wells (wells without an in-place pump). 

The cleaning of submersible pumps and sample tubing along 

with recommendations for additional quality-control samples 

are documented in chapter A7 of the NFM (U.S. Geological 

Survey, variously dated). Depending on the study network, 

wells selected for study were existing wells with in-place 

pumps and in use for domestic or public supply, or for 

purposes such as irrigation and livestock watering; or unused 

wells with or without an in-place pump. These different types 

of wells and conditions call for slightly different techniques 

for obtaining water to test for chemical or microbiological 

constituents.

Water samples were collected at a point as close as 

possible to the well head, thereby avoiding the effects of 

distribution lines, pressure tanks, filtration, or other treatment. 

Thus, the microbiological and other water-quality data 

reported here represent analyses of raw, untreated water only. 

None of these data resulted from analyses of treated finished 

water from distribution systems or at the point of use. As the 

water was withdrawn from the wells, temperature, pH, specific 

conductance, and concentrations of dissolved oxygen were 

monitored until stable values of these properties indicated 

that aquifer water had replaced “old,” standing water within 

the well casing. On reaching stable conditions, final readings 

of the field measurements were recorded and sterile samplecollection bottles were filled for subsequent microbiological 

analyses.

Microbial Analyses and Sources of Data

Water samples for analyses of most fecal-indicator 

bacteria were processed within 6 hours of collection. Samples 

for the analyses of coliphage or C. perfringens were shipped to 

the USGS Ohio Water Microbiological Laboratory (OWML) 

within 24 hours of collection or on the same day of collection 

to meet the laboratory’s hold time criterion of 48 hours to the 

start of analysis (Bushon and others, 2003).

The samples were analyzed for fecal-indicator bacteria 

using membrane-filtration methods, which involve filtering 

known volumes of sample water through a membrane 

filter, placing the filter on a Petri dish of growth medium, 

and incubating the dish for a specified length of time and 

temperature. After incubation, colonies of target organisms 

on the filter were counted and converted to a concentration 

expressed in terms of numbers of organisms per 100 mL 

of sample. During the first cycle of the NAWQA program, 

long-established methods commonly employed were for the 

total-coliform group on mENDO medium (method 9222B, 

American Public Health Association, 1992); the fecal-coliform 

group on mFC medium (method 9222D, American Public 

Health Association, 1992); E. coli on nutrient agar with 4-

methylumbelliferyl-β-D-glucuronide (NA-MUG) medium 

(method 9222G, American Public Health Association, 1992) 

or on mTEC medium (method 1103.1, U.S. Environmental 

Protection Agency, 2002a); and the fecal streptococcus group 

on mKF medium (American Public Health Association, 1992; 

Britton and Greeson, 1988). During Cycle I, investigators 

in some study units also collected samples for analysis of 

concentrations of enterococci bacteria on mE/EIA media 

(method 1106.1, U.S. Environmental Protection Agency, 

2002b) and C. perfringens, which were determined at the 

OWML using membrane-filtration on mCP substrate as 

described in the Information Collection Rule microbial 

laboratory manual (U.S. Environmental Protection Agency, 

1996).

As approved methods using new growth media and 

culturing techniques became available during the Cycle 

II phase of studies, the NAWQA program adopted those 

methods for analysis of fecal-indicator bacteria and viruses 

in ground water. The new methods included use of the 

single-growth medium for simultaneous recovery of the total 

coliforms and E. coli on MI medium (method 1604, U.S. 

Environmental Protection Agency, 2002c) in the field. At the 

OWML, updated methods included testing for the presence or 

absence of somatic and male-specific coliphages by the 2-step 

enrichment procedure (method 1601, U.S. Environmental 

Protection Agency, 2001b).

The fecal-streptococcus, enterococci, and C. perfringens

data were included as part of the inventory of data (fig. 2), 

but they are not part of the discussion of the quality of water 

in principal aquifers or drinking-water supplies because of 

Study Methods 
the small number of tests. In the final data set that included 

replicate quality-control samples for the 22 study units, 1,435 

analytical results for the total-coliform group, 1,338 for 

E. coli, and 836 for coliphage were available for assessing 

the occurrence of fecal-indicator bacteria and virus in ground 

water of different principal aquifers (fig. 2). The water from 

these aquifers was used for various purposes.

Microbiological data collected for the NAWQA program 

and ancillary data including chemical analyses and well 

characteristics can be accessed from the USGS National Water 

Information System (NWIS) data base (http://waterdata.

usgs.gov/nwis), the Data Warehouse (http://infotrek.er.usgs.

gov/traverse/f?p=NAWQA:HOME:9108424999420775073), 

or individual study units (http://water.usgs.gov/nawqa/).

The raw data were simplified and consolidated to create, 

to the extent possible, a consistent and comprehensive final 

data set by study unit, by sampling network, and by principal 

aquifer (table 3). For example, water samples collected from 

wells in the Snake River aquifer in the Upper Snake study unit 

(USNK) were analyzed for only the fecal-coliform group. To 

include discussion of the Snake River aquifer in conjunction 

with other principal aquifers, the results for USNK, with all 

but one sample testing negative for fecal coliforms, were 

compared to E. coli results on the basis that the predominant 

member of the fecal coliform group is the species E. coli (U.

S. Environmental Protection Agency, 1978). Some actions 

involved assigning a well to a principal aquifer or to a 

dominant lithology. These actions were based on several 

sources, including ancillary information available in the USGS 

data bases, the geographic location of the wells and study 

units overlaid on the national maps of principal and major 

aquifers, and the primary lithologies of the principal aquifers 

as assigned by the NAWQA Principal Aquifer regional 

assessment teams (Wayne W. Lapham, U.S. Geological 

Survey, written commun., 2005).

Another consolidation of data involved reducing analyses 

of multiple samples collected at a well to a single analytical 

result so that statistical summaries for all study units and 

principal aquifers were equally weighted on the basis of 

a single value (table 3). These reductions involved data 

collected in the High Plains Ground Water (HPGW), Kanawha 

(KANA), Potomac-Delmarva (PODL), Puget Sound Basin 

(PUGT), Upper Colorado (UCOL), USNK, and lower and 

upper Tennessee (TENN) study units. One approach to data 

consolidation was to select data for a group of wells, such as a 

study network, collected during a particular period, and reject 

samples for the same wells collected outside that period. The 

selected period was chosen to maximize numbers of wells and 

reported results for the study unit or principal aquifer. Another 

approach was to select the data that represented the first visit 

and sampling of a well in a particular network. The first visits 

to wells often equated to the greatest number of wells and 

Figure 2. Numbers of test results for fecal-indicator microorganisms by each analytical method for environmental 

and quality-control samples collected from wells in 22 study units of the National Water-Quality Assessment 

program, 1993–2004.

waI9-0018_fig02

Male-specific, presence/absence

Somatic, presence/absence

Coliphage, presence absence

Clostridium pefringens, by mCP

Enterococci, by mE/EIA

Fecal streptococcus, by mKF

Escherichia coli, by MI

Escherichia coli, by mTEC

Escherichia coli, by NA-MUG

Escherichia coli, all methods

Fecal coliform, by mFC

Total coliform, by MI

Total coliform, by mENDO

Total coliform, all methods

0 200 400 600 800 1000 1200 1400 1600

TARGET ORGANISM AND ANALYTICAL METHOD

TEST RESULTS

419

417

836

52

2

158

804

190

344

1338

414

833

602

1435

 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
samples for a study network. In addition, for discussing the 

quality of ground water by network, water use, or principal 

aquifer, only one result from the pair of samples was used. 

Therefore, if one of the pair tested negative and one tested 

positive for the target organism, the entire well was considered 

to test positive for that organism.

Because of quality-control issues, some analytical results 

for the coliform bacteria and coliphage were excluded from 

the final data set. No coliphage samples collected from wells 

in the KANA, Lake Erie (LERI), Santee (SANT), and UCOL 

study units during 1997–98 and analyzed by quantitative 

methods were used in this report.

Quality Assurance and Quality Control

Prior to water-year 2003, quality-assurance (QA) 

procedures and the collection or preparation of quality-control 

(QC) samples generally followed the guidelines presented in 

Britton and Greeson (1988) and Myers and Sylvester (1997). 

Those guidelines suggest that at a minimum, QC samples 

should include processing filter blanks—one blank at the 

beginning of filtration (an equipment blank) and one blank 

at the end of filtration (a procedure blank), bracketing the 

processing of a water sample. The guidelines also specified 

the use of heat-sensitive indicator tape on all autoclaved 

sample-collection and filtration equipment for monitoring the 

effectiveness of the autoclave and ensuring sterilization of 

equipment.

In water-year 2003, when the NAWQA program 

incorporated microbiology as part of routine sampling 

schedules for Cycle II, additional guidelines that list the types 

of QA procedures and numbers of QC samples appropriate for 

the NAWQA program were put in place (http://oh.water.usgs.

gov/micro/nawqa.html). For fecal-indicator bacteria in ground 

water, the guidelines specify a pair of samples be collected at 

each well and a set of filter blanks be processed to accompany 

every pair of water samples. The filter blanks document 

sterility of the filtration equipment, lack of carryover of cells 

Adjustments made to reduce multiple observations at 

an individual well to a single representative value

Adjustments and assumptions taken to populate 

selected data fields with missing values

HPGW:

Removed 1 of 2 samples in June 2004 and retained the sample with 

an analysis of coliphage virus

CCYK:

For the SWQA network, principal aquifer assumed to be Columbia 

Plateau and primary lithology as volcanic (basalt)

KANA:

Removed 1 of 2 pairs of samples (multiple quality-control samples) 

from 1 well

CONN:

Lithology assumed to be sand or sand and gravel

PODL:

Removed 1 sample in 2004 from 1 well and retained the earlier 2001 

sample, which was part of a larger set of results

GAFL:

For wells listed as cased test hole, assumed to be unused; lithology 

assumed to be limestone

PUGT:

Removed the August 1998 samples and retained the March 1998 

samples, which were part of larger sets of results for two land-use 

study networks.

SANJ:

For SWQA, lithology assumed to be alluvium

CCYK:

Removed the October 1997 samples and retained the first set of 

samples collected in March-April 1997 for an urban land-use 

study network.

TRIN:

For some MAS-3 network wells, lithology assumed to be sand

USNK:

For 42 of 82 wells in 1994 and 1995, retained the August monthly 

samples, some of which had corresponding chemical analyses.

USNK:

Lithology for 3 wells assumed to be basalt/volcanic and for 1 well, 

sand and gravel

TENN:

Removed a 2001 sample from 5 wells and retained the 2000 samples, 

which were part of a larger set of data

WMIC:

Lithology for 2 wells assumed to be sand and gravel

Table 3. Consolidations and adjustments to the raw microbiological and associated ground-water data by study unit and network, 

water use, principal aquifer, and lithology.

[Abbreviations: CCYK, Central Columbia Plateau-Yakima; CONN, Connecticut; GAFL, Georgia-Florida; HPGW, High Plains; KANA, Kanawha; PODL, 

Potomac-DelMarva; PUGT, Puget Sound Basin; SANJ, San Joaquin; TENN, lower and upper Tennessee; TRIN, Trinity; USNK, Upper Snake River; WMIC, 

Western Lake Michigan; MAS, major aquifer study; SWQA, source-water quality assessment]

Study Methods   
between filtrations, and whether cells are lost to the walls 

of the filtration equipment due to incomplete rinsing. The 

guidelines also specify processing of field blanks and of 

positive and negative control samples at frequencies depending 

on numbers of wells sampled. Processing of field blanks 

involves passing sterile water through all parts of collection 

equipment, from the pump (if applicable) through the tubing 

and into the sample bottles. Positive and negative control 

samples are pure cultures of target organisms that ensure the 

quality of media and reagents for use. The control samples are 

processed by the membrane filtration method and the results 

are evaluated for proper recovery and growth of the positivecontrol organism and lack of growth by the negative-control 

organism. In addition to the QC samples for the fecal-indicator 

bacteria, field blanks are prepared for coliphage analysis, 

and replicate samples are collected and spiked with target 

organisms at the laboratory to determine if there are matrix 

interferences in the analysis.

At the time of this data compilation, selected QC data 

were obtained from nine Cycle II study units for evaluating 

the set of microbiological data for the purposes of this report. 

QC data were not requested from the Cycle I study units 

because these data do not exist in electronic data bases and so 

are not easily constructed from archived files. For the Cycle II 

data, target organisms were detected in only 13 of 379 filter 

blanks (3.4 percent). For the individual study units reporting 

filter-blank data, detection rates ranged from 1 to 12 percent 

of the blanks prepared. The QC guidelines state that if target 

colonies in the filter blank are less than 5 percent of the 

colony count of the environmental sample, the results for the 

sample are accepted. If target colonies on the filter blank are 

greater than 20 percent of the target colonies of the sample, 

the results are rejected. For target colonies that amount to 5 to 

20 percent of a sample’s colony count, the concentration value 

in NWIS is assigned a remark code of V (value affected by 

contamination), a value-qualifier code of W (high variability), 

and a result-level comment indicating the number of target 

colonies in the filter blank. Evaluation of the filter blank 

data resulted in rejecting five sample results (including any 

replicates) for the total coliform group. During their wellnetwork sampling, five Cycle II study units processed field 

blanks, all of which were negative for target organisms. 

Analyses of these filter- and field-blank samples indicated 

that equipment sterilization, sampling procedures, and sample 

handling and filtration were effectively controlled and thus 

resulted in a set of high-quality data for describing the quality 

of the ground-water resources.

NAWQA staff in eight of the Cycle II study units 

consistently collected and processed duplicate samples for 

each well. The relative percent differences in the analytical 

results for 402 pairs of samples ranged from 0 to 200 percent. 

The average and median relative percent differences were 

13 and 0, respectively. Most pairs (338) had the same value, 

which results in percent differences of zero.

Statistical Analyses

Graphical analyses of the data set through the use of box 

plots, notched box plots, scatter plots, and bar charts were 

used to evaluate the occurrence, distribution, and potential 

relations of the fecal-indicator bacteria in ground water with 

other constituents or with well characteristics. Box plots 

display summaries of the distribution of a group of data by 

showing the center location (median), the variation through the 

height of the box (interquartile range of values), the skewness 

through the relative size of the box halves, and extreme values 

or outliers of the data (Helsel and Hirsch, 1992). Notched 

box plots portray the same information and also show the 

95-percent confidence interval about the median. Boxes 

with nonoverlapping notches indicate significant differences 

between the groups of observations (McGill and others, 1978). 

Scatter plots can indicate patterns in a group of data, such as 

correlation or trend relations. Bar charts are mostly used in 

this report to display numbers of observations or frequencies 

of bacterial detections.

Nonparametric statistical testing by the Kruskal-Wallis 

test and Wilcoxon rank-sum test was used to examine the 

data for significant differences between groupings of coliform 

bacteria concentrations or detections within study networks, 

classes of water use, principal aquifers, or types of lithology. 

The null hypothesis of the Kruskal-Wallis test states that 

the rank of the median (or mean) of the data for each group 

is identical, and the alternative hypothesis is that at least 

one group differs in its distribution, which tends to produce 

observations (concentrations) different in value (Helsel and 

Hirsch, 1992). The Kruskal-Wallis test does not determine 

which group or groups are different. For this, the Wilcoxon 

rank-sum test was used with significance levels adjusted for 

the total number of tests performed within each group of data, 

or notched box plots helped to identify statistically different 

groups within the groupings of interest.

For statistical testing of concentration data, values 

reported as < (less than) 1 CFU/100mL (colony forming unit 

per 100 milliliters) in the USGS NWIS database were treated 

as zeroes. This assumption was because no organisms were 

found on the filter and media; therefore the count for that test 

was zero organisms. Statistical tests were also performed with 

coliform bacteria data expressed as detections (with positive 

results set to equal 1) or nondetections (with negative results 

set to equal 0), and with coliphage data, which are coded in 

NWIS as a 1 (for present in the sample) or a 2 (for absent in 

the sample).

10 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
Microbial Quality of Water in Principal 

Aquifers

Testing was done for fecal-indicator bacteria and 

coliphages on samples from at least 15 wells in the 22 study 

units during Cycle I or Cycle II of the NAWQA program. 

Concentrations and detection frequencies of fecal-indicator 

bacteria and coliphage are summarized by study networks 

and by principal aquifers and their lithology. The occurrence 

of these microorganisms in water supplies and relations 

to selected well and water-quality characteristics are also 

discussed.

The 22 study units collected samples from 1,205 wells 

as part of the MAS, LUS, and SWQA sampling networks. 

Concentrations of fecal-indicator bacteria in 1,174 of these 

wells were used in the analyses described in this report. 

Samples collected from 450 wells in 11 of the 22 study units 

were analyzed for the presence of coliphage. Coliphage data 

from 423 of those wells were available for this analysis.

The study wells are completed in 16 principal aquifers 

and 7 types of lithology. Water-use types for these wells were 

originally coded by study-unit staff within 1 of 15 categories, 

including drinking-water supply (domestic or public), water 

used for power or aquaculture, and water use designated as 

“other” or ”unused.” For this report, several of the minor 

types of water use were combined—commercial, industrial, 

institutional, and recreational into one class; irrigation and 

stock watering into a second class; and a third class referred 

to simply as “other.” Water-use types described in this report 

include these three combined classes and the classes termed 

domestic, public, and unused.

Detection frequencies and concentrations of totalcoliform bacteria were significantly different (p-value <0.05) 

among the study networks, principal aquifers, types of 

lithology, and water-use classes. These differences are further 

examined in the discussions of the microbial quality of ground 

water sampled for the NAWQA program.

Fecal-Indicator Bacteria and Coliphage 

Viruses in Study-Unit Well Networks and 

Principal Aquifers

Fecal-indicator bacteria were geographically widespread, 

with at least one well testing positive among all the wells 

sampled within each study unit and principal aquifer (fig. 3A

and 3B). Coliphage, which occur less frequently than the 

bacteria, were present in well samples from 4 of the 11 

study units that sampled and tested for coliphage—the 

Central Columbia Plateau–Yakima (CCYK), Georgia-Florida 

(GAFL), San Joaquin (SANJ), and Trinity (TRIN) study units, 

representing the Columbia Plateau, Floridan, Central Valley, 

and Coastal Lowlands aquifers, respectively.

Samples from 347 wells (29.6 percent of the 1,174 wells 

for which data were used in this analysis) tested positive 

for fecal-indicator bacteria (either total coliform, E. coli, or 

fecal coliform). Individual study-unit detection frequencies 

ranged from 1 out of 82 well samples (1 percent) in the USNK 

testing positive for fecal coliforms to 108 out of 155 samples 

(70 percent) in the LSUS testing positive for total coliforms 

(fig. 4). The greatest number of wells that tested positive 

for E. coli was in the TENN study unit; 32 out of 124 wells 

(26 percent) tested positive.

Concentrations of total coliforms in samples from 

the 1,174 wells ranged from <1 to 1,600 CFU/100mL and 

concentrations of E. coli ranged from <1 to 1,200 CFU/

100mL. Median concentrations for both total coliforms and 

E. coli were at the reporting limit of <1 CFU/100mL. In 

addition, 67 percent of total coliform and 85 percent of E. coli

concentrations were at the minimum reporting limit, indicating 

that most concentrations are low.

With 61 percent of all the wells sampled, the MAS is the 

largest of the three major study networks, followed by the LUS 

network and the SWQA network (table 4). For the MAS, totalcoliform concentrations for 566 wells; E. coli concentrations 

for 592 wells; and coliphage results for 280 wells were used 

in this analysis (table 4). For the LUS network, concentrations 

of total coliforms and E. coli were available for 251 wells and 

237 wells, respectively. For all three networks, the highest 

percentage of total coliform detections (50.2 percent) occurred 

in wells in the LUS network, and in the agricultural LUS 

network, total coliforms were detected in 67.2 percent of the 

wells (fig. 5A). In contrast with the LUS network, the lowest 

percentage of total-coliform detections (19.5 percent) occurred 

in wells in the SWQA network. Median concentrations of 

coliform bacteria were <1 CFU/100mL for the MAS and 

SWQA networks, 1 CFU/100mL for the LUS network, and 

4 CFU/100mL for the agricultural LUS network. Excluding 

the high concentration of coliform bacteria in a sample from 

one well, total coliform concentrations were equal to or less 

than 420 CFU/100mL and E. coli concentrations were equal to 

or less than 440 CFU/100mL (fig. 5B).

Microbial Quality of Water in Principal Aquifers 11
wa19_0018_fig03a&b

Glacial Deposits

EXPLANATION

California Coastal Basins

Central Valley

Columbia Plateau

Snake River

Basin and Range

Denver Basin

High Plains

Edwards-Trinity

Cambrian-Ordovician

Mississippi Embayment- Texas Coastal Uplands

Coastal Lowlands

Floridan

Biscayne

Piedmont and Blue Ridge

North Atlantic Coastal Plain

New York, New England

Mississippian-Pennsylvanian

Ozark Plateaus

Southeastern Coastal Plain

Valley and Ridge

Stream and River Valley (UCOL, YELL; unknown extent)

Ordovician (Lower Tennessee; unknown extent)

Regions of future microbial data collection

Fecal-indicator bacteria wells--open circle is no detection; filled circle is detection

Major Aquifer Study wells

Land Use Study wells

Source-Water Quality Assessment wells

Surficial Aquifer System is not shown.

Principal aquifers modified from Lapham and others, 2005

A

B

Figure 3. Locations of wells in principal aquifers that tested positive for fecal-indicator bacteria (A) and wells where fecalindicator bacteria were not detected in samples collected for the National Water-Quality Assessment program (B), 1993–2004.

12 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
waI9-0018_fig04

0

20

40

60

80

100

120

140

160

180

STUDY UNIT

NUMBER OF WELLS

LSUS

KANA

GAFL

PODL

TENN

PUGT

HPGW

SANJ

DELR

UCOL

ACAD

LERI

TRIN

CCYK

WMIC

SANT

YELL

CONN

NVBR

WHMI

MOBL

USNK

155

86

58

65

124

27

70

28

46

68

21

26

41

44

28

25

28

45

62

15

30

82

108

33

32

27

17

14

12

1111

9

6

6

5

8

4

3

333

2

00

32

55

7

32

6

2

11

0

3

0

4

00000

1

0

2

1

Number of samples

Number of total-coliform detections

Number of Escherichia coli detections

Figure 4. Number of wells sampled and number of wells with detections of coliform bacteria in samples collected in 

22 study units of the National Water-Quality Assessment program, 1993–2004. (See table 2 for explanation of study-unit 

name abbreviations.)

Table 4. Summary of microbiological data collected from wells in major aquifer study, land-use 

study, and source-water quality assessment networks in 22 study units of the National Water-Quality 

Assessment Program, 1993–2004.

[Study network: MAS, major-aquifer study; LUS, land-use study; SWQA, source-water quality assessment. 

Abbreviations: CFU/100mL, colony-forming units per 100 milliliters. Symbols: <, less than; >, greater than; –, no value]

Tests Study network Number 

of wells

Number of wells 

with detections 

(percentage)

Concentration 

(CFU/100mL)

Median Range

Total coliform MAS 566 162 (28.6) <1 <1 – 1,600

LUS, all 251 126 (50.2) 1 <1 – 420

LUS, agriculture 119 80 (67.2) 4 <1 – >80

LUS, urban 77 27 (35.1) <1 <1 – 110

SWQA 149 29 (19.5) <1 <1 – >80

Escherichia coli MAS 592 51 (8.6) <1 <1 – 1,200

LUS, all 237 50 (21.1) <1 <1 – >80

LUS, agriculture 112 34 (30.4) <1 <1 – >80

LUS, urban 70 12 (17.1) <1 <1 – >80

SWQA 149 3 (2.0) <1 <1 – 2

Coliphage MAS 280 9 (3.2) – –

LUS, all 3 0 (0) – –

LUS, agriculture 2 0 (0) – –

LUS, urban 1 0 (0) – –

SWQA 140 5 (3.6) – –

1

Includes Upper Snake River (USNK) wells sampled for fecal coliforms.

Microbial Quality of Water in Principal Aquifers 13
Of the 16 principal aquifers studied by the NAWQA 

program during 1993–2004, the number of wells testing 

positive for coliform bacteria exceeded 50 percent in three 

aquifers—the Valley and Ridge, Floridan, and the Piedmont 

and Blue Ridge (fig. 6A and table 5). The lowest detection 

frequencies of coliform bacteria (less than 5 percent) among 

the 16 principal aquifers were in samples from wells in the 

Basin and Range and Snake River aquifers (fig. 6A, table 5). 

Detection frequencies of total coliform bacteria for the Valley 

and Ridge, Floridan, and Piedmont and Blue Ridge aquifers 

were significantly higher (p-value <0.0006) than detection 

frequencies for the Glacial Deposits, Columbia Plateau, 

High Plains, Stream and River Valley, Coastal Lowlands, 

Southeastern Coastal Plain, and Basin and Range aquifers 

(fig. 6B).

For the large MAS network, the frequency of wells 

testing positive for total coliform was 82 percent for the 

Central Valley aquifer (fig. 7A); however, this high frequency 

of detection might be a function of the low number of 

available samples. Detection frequencies of E. coli were 

highest for MAS wells in the Ordovician aquifer (30 percent), 

followed by detections in the Central Valley (25 percent) 

and the Mississippian-Pennsylvanian (19 percent) aquifers 

(fig. 7A).

waI9-0018_fig05

0

10

20

30

40

50

60

70

80

90

100

Major

Aquifers

(MAS)

Land Use

(LUS)

Land Use–

Agriculture

Land Use–

Urban

SourceWater Quality

Assessment

(SWQA)

Major

Aquifers

(MAS)

Land Use

(LUS)

SourceWater Quality

Assessment

(SWQA) STUDY NETWORK

DETECTIONS OF COLIFORM BACTERIA, IN PERCENT 

Number of detections / Number of wells

A

1

10

100

1000

CONCENTRATION,

IN COLONY-FORMING UNITS PER 100 MILLILITERS

B

566 592 251 237 149 149

566 Number of values 

1.5 X interquartile

 range

1.5 X interquartile

 range

75th percentile

Median

25th percentile

Lower detached

Lower outside

Upper detached

Upper outside

Escherichia coli

EXPLANATION 

Total coliform

SCHEMATIC BOXPLOT

x

x

162/566

126/251

80/119

27/77

29/149

51/592

50/237

34/112

12/70

3/149

Total coliform

Escherichia coli

Figure 5. Percentage of wells testing positive for total coliform bacteria and Escherichia coli (A), and concentrations of 

coliform bacteria (B) by study network in samples collected in 22 study units of the National Water-Quality Assessment 

program, 1993–2004.

The Piedmont and Blue Ridge, Floridan, Coastal 

Lowlands, Columbia Plateau, Glacial Deposits, Basin and 

Range, and Central Valley aquifers, or just less than one-half 

the 16 aquifers studied since 1993, were the first principal 

aquifers to be sampled as part of the new SWQA network 

of NAWQA Cycle II. Samples with the highest detection 

frequencies of total coliforms were collected from Piedmont 

and Blue Ridge wells (greater than 50 percent) followed by 

detections in samples from wells completed in the Floridan 

aquifer (30 percent). Detection frequencies of E. coli were 

low, however, with nondetections reported for all wells in 4 

of the 7 aquifers and only one detection in each of the others 

(fig. 7B).

Distribution of coliform bacteria concentrations was 

highly influenced by many samples that tested negative; 

and, of the samples that tested positive, many concentrations 

were near the minimum reporting limit (fig. 8). More than 

75 percent of total coliform and E. coli concentrations in 

samples from 9 of the 16 aquifers were <1 CFU/100mL. 

Concentrations of total coliforms tended to be distributed 

somewhat higher in samples from four aquifers: 25 percent of 

the concentrations ranged from 1 to 7 CFU/100 mL in samples 

from the Floridan aquifer; from 1 to 4 CFU/100 mL in 

samples from the Piedmont and Blue Ridge aquifer; from <1 

to 4 CFU/100 mL in samples from the North Atlantic Coastal 

Plain aquifer; and from <1 to 2 CFU/100 mL in samples from 

the Central Valley aquifer.

14 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
waI9-0018_fig06

Number of wells with detections / Number of samples

Valley and RidgeFloridanPiedmont and Blue RidgeCentral ValleyMississippian-PennsylvanianNorth Atlantic Coastal PlainMississippi/Texas Coastal UplandsGlacial DepositsColumbia PlateauHigh PlainsStream and River ValleyCoastal Lowlands

Southeastern Coastal Plain

Basin and Range

Valley and Ridge

Floridan

Piedmont and Blue Ridge

Central Valley

Mississippian-Pennsylvanian

North Atlantic Coastal Plain

Mississippi/Texas Coastal Uplands

Glacial Deposits

Columbia Plateau

High Plains

Stream and River Valley

Coastal Lowlands

Southeastern Coastal Plain

Basin and Range

A

B

0

10

20

30

40

50

60

70

55/104

11/28 22/57 19/50

9/30 6/21

38/170

8/44

8/55

12/96 3/25 5/41

3/62

1/82

95/155

32/58

Valley and Ridge

Piedmont and Blue Ridge

Central Valley

Mississippian-Pennsylvanian

North Atlantic Coastal Plain

Ordovician (lower Tennessee)

Mississippi EmbaymentTexas Coastal Uplands

Glacial Deposits

Columbia Plateau

High Plains

Stream and River Valley

Coastal Lowlands

Southeastern Coastal Plain

Basin and Range

Floridan

Snake River

PRINCIPAL AQUIFER

DETECTIONS OF COLIFORM BACTERIA,IN PERCENT

Total coliform bacteria

Escherichia coli

Fecal coliform bacteria

EXPLANATION

Significant difference at p-value <0.0006

Difference not significant

Figure 6. Percentage of wells testing positive for coliform bacteria (A), and significantly different (p-value <0.0006) 

detection frequencies of total coliform bacteria (B) by principal aquifer from data collected in 22 study units of the National 

Water-Quality Assessment program, 1993–2004.

Microbial Quality of Water in Principal Aquifers 15
Table 5. Summary of microbiological data collected from wells in each principal aquifer in 22 study units of the National 

Water-Quality Assessment Program, 1993–2004.

[Abbreviations: CFU/100mL, colony-forming units per 100 milliliters. Symbols: <, less than; >, greater than; –, no data or not applicable]

Tests Principal aquifer Number 

of wells

Number of wells 

with detections 

(percentage)

Concentration 

(CFU/100mL)

Median Range

Total coliform Valley and Ridge 155 95 (61.3) 2 <1 – 1,600

Mississippian-Pennsylvanian 57 22 (38.6) <1 <1 – 420

Glacial Deposits 170 38 (22.4) <1 <1 – 110

Floridan 58 32 (55.2) <1 <1 – >80

Piedmont and Blue Ridge 104 55 (52.9) <1 <1 – >80

North Atlantic Coastal Plain 50 19 (38.0) <1 <1 – >80

Mississippi Embayment-Texas Coastal Uplands 21 6 (28.6) <1 <1 – 75

Central Valley 28 11 (39.3) <1 <1 – 63

Stream and River Valley 96 12 (12.5) <1 <1 – 60

Southeastern Coastal Plain 25 3 (12.0) <1 <1 – 25

Coastal Lowlands 41 5 (12.2) <1 <1 – 20

Columbia Plateau 44 8 (18.2) <1 <1 – 18

High Plains 55 8 (14.5) <1 <1 – 18

Basin and Range 62 3 (4.8) <1 <1 – 5

Ordovician (lower Tennessee) 0 – – –

Snake River 0 – – –

Escherichia coli Valley and Ridge 113 39 (34.5) <1 <1 – 1,200

Ordovician (lower Tennessee) 30 9 (30.0) <1 <1 – 440

Mississippian-Pennsylvanian 121 18 (14.9) <1 <1 – 340

Snake River 82 1 (1.2) <1 <1 – 90

Piedmont and Blue Ridge 63 4 (6.3) <1 <1 – 38

Southeastern Coastal Plain 35 2 (5.7) <1 <1 – 23

High Plains 55 2 (3.6) <1 <1 – 18

Mississippi Embayment-Texas Coastal Uplands 21 3 (14.3) <1 <1 – 15

Central Valley 19 1 (5.3) <1 <1 – 13

North Atlantic Coastal Plain 50 6 (12.0) <1 <1 – 8

Coastal Lowlands 41 4 (9.8) <1 <1 – 8

Glacial Deposits 146 8 (5.5) <1 <1 – 8

Floridan 60 5 (8.3) <1 <1 – 1

Basin and Range 62 1 (1.6) <1 <1 – 1

Stream and River Valley 36 0 (0) <1 –

Columbia Plateau 44 0 (0) <1 –

16  Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
waI9-0018_fig07

2/46

4/43

2/27

3/25

13/28

30/59

9/11

40/89

10/29

6/21

6/29

6/30

12/74

8/55

3/27

0/50/4

2/55

0/63

12/62

0/29

3/21

2/29

1/4

3/49

4/30

10/60

1/46

1/79

9/30

0/46

3/28

2/27

2/30

0/240/19

2/21

0/280/57

0

10

20

30

40

50

60

70

80

90

100

PRINCIPAL AQUIFERS OF THE MAJOR AQUIFER STUDIES (MAS)

PERCENTAGE OF WELLS WITH DETECTIONS

0

10

20

30

40

50

60

70

80

90

100

PERCENTAGE OF WELLS WITH DETECTIONS

Number of wells with detections / Number of samples

A

3/14

9/30

8/15

2/156/45

1/15

0/450/150/150/15

1/15

1/30

1/14

0/120/150/15

0/38

0/26

1/15

4/30

0/15

PRINCIPAL AQUIFERS OF THE SOURCE-WATER QUALITYASSESSMENTS (SWQA)

B

Central Valley

Piedmont and Blue Ridge

Floridan

Valley and Ridge

North Atlantic Coastal Plain

Mississippi EmbaymentTexas Coastal Uplands

Columbia Plateau

Mississippian-Pennsylvanian

Glacial Deposits

High Plains

Southeastern Coastal Plain

Stream and River Valley

Coastal Lowlands

Basin and Range

Snake River

Ordovician (lower Tennessee)

Total coliform

Escherichia coli

Coliphage

Piedmont and Blue Ridge

Floridan

Coastal Lowlands

Columbia Plateau

Glacial Deposits

Basin and Range

Central Valley

High Plains

Southeastern Coastal Plain

Stream and River Valley

Mississippi EmbaymentTexas Coastal Uplands

North Atlantic Coastal Plain

Valley and Ridge

Mississippian-Pennsylvanian

Snake River

Ordovician (lower Tennessee)

Figure 7. Percentage of detections of coliform bacteria and coliphage virus in wells sampled as part of the major aquifer studies 

(A) and source-water quality assessments (B) for the National Water-Quality Assessment program, 1993–2004.

Microbial Quality of Water in Principal Aquifers 17
Maximum concentrations of total coliforms of 

1,600 CFU/100mL and of E. coli of 1,200 CFU/100mL were 

detected in a sample from a well completed in carbonate 

rocks (dolomite) of the Valley and Ridge aquifer. This 

aquifer also had the highest overall concentrations of total 

coliform bacteria, with a median of 2 CFU/100mL (table 5) 

and 25 percent of the concentrations ranging from 2 to 

34 CFU/100mL (fig. 8). High concentrations of coliform 

bacteria (greater than 300 CFU/100mL) also were detected 

in samples from the Mississippian-Pennsylvanian and 

Ordovician aquifers. For wells in the Floridan, Piedmont and 

Blue Ridge, and North Atlantic Coastal Plain aquifers, high 

concentrations were reported only to the upper limit of the 

analytical method (80 CFU/100mL) for an undiluted sample, 

so the maximum concentrations are unknown. For the MAS, 

however, the aquifers with the highest overall concentrations 

of total coliform bacteria were the Floridan, with a median 

of 4 CFU/100mL, and the Central Valley, with a median of 

3 CFU/100mL.

wa9BI99_01_fig08

Upper reporting level (no dilutions)

Minimum

reporting

level

1

10

100

1000

Valley and Ridge

MississippianPennsylvanian

Glacial Deposits

Floridan

Piedmont and

Blue Ridge

North Atlantic

Coastal Plain 

Mississippi Embayment-

 Texas Coastal Uplands

Central Valley

Stream and River Valley

Southeastern

Coastal Plain

Coastal Lowlands

Columbia Plateau

High Plains

Basin and Range

Ordovician

(lower Tennessee)

Snake River

CONCENTRATION, IN COLONY FORMING UNITS PER 100 MILLILITERS

PRINCIPAL AQUIFER

155 113 57 121 170 146 58 60 104 63 50 50 21 21 28 19 96 36 25 35 41 41 44 44 55 55 62 62 0 30 0 82

155 Number of values 

1.5 X interquartile

 range

1.5 X interquartile

 range

75th percentile

Median

25th percentile

Lower detached

Lower outside

Upper detached

Upper outside

Escherichia coli

EXPLANATION 

Total coliform

SCHEMATIC BOXPLOT

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

Figure 8. Concentrations of total coliform and Escherichia coli by principal aquifer in samples collected in 22 study units 

of the National Water-Quality Assessment program, 1993–2004.

18  Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
12/111

10/48 61/301

30/112

45/118

38/74

121/202

0

10

20

30

40

50

60

70

AQUIFER LITHOLOGY

Carbonate rocksCrystalline rocksSandstone, ShaleVolcanic

Semiconsolidated sand

Sand, gravelAlluvium

Carbonate rocks

Crystalline rocks

Sandstone, Shale

Volcanic

Semiconsolidated sand

Sand, gravel

Alluvium

DETECTIONS OF COLIFORM BACTERIA, IN PERCENT

Semiconsolidated sand, residuum

Carbonate rocks

Crystalline rocks

Volcanic

Sand, Gravel

Alluvium

Sandstone, Shale

A

B

Number of wells with detections /

Number of samples

Coliform bacteria

EXPLANATION

Significant difference at p-value <0.002

Difference not significant

Figure 9. Percentage of wells testing positive for coliform bacteria (A), and significantly different detection 

frequencies (p-value <0.002) of total coliform bacteria with respect to aquifer lithology (B). Graphs are based 

on data collected in 22 study units of the National Water-Quality Assessment program, 1993–2004.

Detection of Coliform Bacteria in Principal 

Aquifers of Different Lithologies

Variations in the detection frequencies of coliform 

bacteria and in the distribution of their concentrations among 

principal aquifers are explained in part by types of lithology. 

Detection frequencies were greater for wells in carbonate 

rocks (primarily limestone and dolomite), crystalline rocks 

(primarily undifferentiated metamorphic rocks and schist) 

or sandstone, shale, undifferentiated sedimentary rocks, than 

for wells in unconsolidated materials (different mixtures of 

sand, gravel, and clay, or alluvium), semiconsolidated sand, 

or volcanic rocks (basalt, with sand and gravel interbeds) 

(fig. 9A). More than 50 percent of all sampled wells completed 

in carbonate rocks, such as those that make up part of the 

of the Valley and Ridge, the Floridan, and the Piedmont 

and Blue Ridge aquifers (table 2), or in crystalline rocks of 

the Piedmont and Blue Ridge aquifers tested positive for 

coliform bacteria (fig. 9A, table 6). The frequency of detection 

of coliform bacteria in wells completed in unconsolidated 

materials tends to be relatively low (less than about 

20 percent), and is significantly lower (p-value <0.002) than 

detections for wells completed in consolidated rocks (fig. 9B). 

Principal aquifers composed primarily of these unconsolidated 

materials and with low detection frequencies include the Basin 

and Range, Coastal Lowlands, Southeastern Coastal Plain, 

Stream and River Valley, and High Plains.

Relatively high concentrations of fecal-indicator bacteria 

were detected in wells completed in carbonate rocks, with 

25 percent of the total-coliform values ranging from 1 to 

24 CFU/100mL (fig. 10). Carbonate-rock aquifers with 

high concentrations of total coliforms or E. coli include the 

Floridan, the Ordovician in the lower Tennessee region, 

the Valley and Ridge, the Piedmont and Blue Ridge, and 

the Mississippian-Pennsylvanian. Concentrations of total 

coliforms in unconsolidated materials were generally low, with 

medians of <1 CFU/100mL.

Microbial Quality of Water in Principal Aquifers 19
Table 6. Summary of microbiological data, by type of principal-aquifer lithology, collected from wells in 22 study units 

of the National Water-Quality Assessment program, 1993–2004.

[Type of lithology: residuum, remains from chemical and physical weathering of parent aquifer materials or formation. Abbreviations: 

CFU/100mL, colony-forming units per 100 milliliters; <, less than; >, greater than; –, no data or not applicable]

Tests Type of lithology Number 

of wells

Number of wells 

with detections

(percentage)

Concentration

(CFU/100mL)

Median Range

Total coliform Carbonate rocks (limestone, dolomite) 202 121 (59.9) 2 <1 –1,600

Sandstone, shale 118 45 (38.1) <1 <1 – 420

Crystalline rocks 74 38 (51.4) 1 <1 – >80

Semiconsolidated sand, residuum 112 30 (26.8) <1 <1 – >80

Volcanic 48 10 (20.8) <1 <1 – >18

Sand, gravel 301 61 (20.3) <1 <1 – >110

Alluvium 111 12 (10.8) <1 <1 – 60

Escherichia coli Carbonate rocks (limestone, dolomite) 253 65 (25.7) <1 <1 –1,200

Volcanic 130 2 (1.5) <1 <1 – 90

Crystalline rocks 63 4 (6.3) <1 <1 – 38

Sand, gravel 280 13 (4.6) <1 <1 – 23

Semiconsolidated sand, residuum 112 13 (11.6) <1 <1 – 15

Sandstone, shale 89 7 (7.9) <1 <1 – 33

Alluvium 51 0 (0) <1 –

Coliphage Semiconsolidated sand, residuum 86 3 (3.5) – –

Volcanic 40 2 (5.0) – –

Carbonate rocks (limestone, dolomite) 78 6 (7.7) – –

Sand, gravel 192 2 (1.0) – –

Crystalline rocks 12 0 (0) – –

Sandstone, shale 0 – – – –

Alluvium 15 1 (6.7) – –

1

10

100

1000

CONCENTRATION,

IN COLONY-FORMING UNITS PER 100 MILLILITERS

Carbonate

rocks

Crystalline

rocks

Sandstone,

shale

Volcanic Sand,

gravel

Semiconsolidated

sand,

residuum

Alluvium

202 253 74 63 118 89 48 130 112 112 301 280 111 51

202 Number of values 

1.5 X interquartile

 range

1.5 X interquartile

 range

75th percentile

Median

25th percentile

Lower detached

Lower outside

Upper detached

Upper outside

Escherichia coli

EXPLANATION 

Total coliform

SCHEMATIC BOXPLOT

x

x

x

x

xx

x

x

x

x

xx

x

xx

Figure 10. Concentrations of total coliform and Escherichia coli by principal aquifer lithology 

in samples collected in 22 study units of the National Water-Quality Assessment program, 

1993–2004.

20 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
Water Use, Drinking-Water Supplies, and Wells 

of the Major Aquifer Study and Source-Water 

Quality Assessment Networks

The MAS and SWQA study networks focused on the 

quality of ground water used for drinking-water supplies 

through the sampling of about 630 wells used for domestic and 

public supplies. Total coliforms were detected in 27 percent 

and E. coli in 6 percent of these wells. Most (71 percent) of 

the MAS wells were domestic wells; however, an additional 

15 percent of MAS wells were used for public supplies 

(fig. 11). Conversely, and by study design, nearly all of the 

SWQA wells were used for public supplies. A few SWQA 

wells, however, were described as unused at the time of 

sampling and one was described as a domestic well (fig. 11).

Of the 6 classes of water use considered in this analysis, 

wells used for domestic purposes made up the largest class, 

with data on total-coliform concentrations available for 

405 wells and on E. coli concentrations for 397 wells. The 

domestic-use class was followed by public supply and unused 

classes with total-coliform concentrations for 227 and 37 

wells, respectively (table 7). Total coliforms were detected in 

33 percent of the samples from domestic wells and 16 percent 

of samples from public supply wells, and E. coli were detected 

in 8 and 3 percent of samples from domestic and public supply 

wells, respectively (fig. 12A).

Median concentrations of total coliforms and E. coli

were at the detection limit of <1 CFU/100mL for all 6 classes 

of water use (fig. 12B, table 7); however, the concentrations 

in domestic wells were significantly higher (p-value <0.05) 

than concentrations in public-supply wells. In samples 

from domestic wells, the maximum concentrations of total 

coliforms and E. coli were 1,600 and 1,200 CFU/100mL, 

respectively. Maximum concentrations of total coliforms 

detected in samples from public-supply wells were >80 

CFU/100mL for a well completed in the Floridan aquifer 

of the GAFL study unit, and 61 CFU/100mL for a well 

completed in the Glacial Deposits aquifer of the HPGW study 

unit. More than 75 percent of samples from domestic wells 

had concentrations of total coliforms of 2 CFU/100mL or 

less. In samples from public-supply wells, however, more than 

75 percent of concentrations of total coliforms were less than 

the minimum report level of <1 CFU/100mL (fig. 12B).

Figure 11. Percentage of major aquifer study (MAS) and source-water quality 

assessment (SWQA) wells sampled by class of water use in 22 study units of the 

National Water-Quality Assessment program, 1993-2004.

0

10

20

30

40

50

60

70

80

90

100

Domestic Public Other Unused

CLASS OF WATER USE

PERCENTAGE OF WELLS SAMPLED

Commercial,

Industrial,

Institututional,

Recreation

Irrigation,

Stock

Major aquifer studies (MAS) 566 samples

Source-water quality assessments (SWQA) 149 samples

71

95

1

15

5

0 2 0 1 0

5 4

Microbial Quality of Water in Principal Aquifers 21
Table 7. Summary of microbiological data collected from major aquifer study and source-water-quality 

assessment wells used for domestic, public supply, and other purposes, and from unused wells by the 

National Water-Quality Assessment Program, 1993–2004.

[Abbreviations: CFU/100mL, colony-forming units per 100 milliliters; coliphage reported as present or absent only. 

Symbols: <, less than; >, greater than; –, no data or not applicable]

Tests Water use Number of 

wells 

Number of 

detections 

(percentage)

Concentration

(CFU/100mL)

Median Range

Total coliform Domestic 405 134 (33.1) <1 <1 – 1,600

Public 227 36 (15.9) <1 <1 – >80

Commercial, industrial, 

institution, recreation

27 9 (33.3) <1 <1 – >80

Irrigation, stock 12 3 (25.0) <1 <1 – 25

Other 7 1 (14.3) <1 <1 – 1

Unused 37 8 (21.6) <1 <1 – 178

Escherichia coli Domestic 397 31 (7.8) <1 <1 – 1,200

Public 220 6 (2.7) <1 <1 – 14

Commercial, industrial, 

institution, recreation

24 1 (4.2) <1 <1 – 6

Irrigation, stock 38 3 (7.9) <1 <1 – 440

Other 14 4 (28.6) <1 <1 – 14

Unused 48 9 (18.8) <1 <1 – 68

Coliphage Domestic 200 7 (3.5) – –

Public 183 5 (2.7) – –

Commercial, industrial, 

institution, recreation

6 1 (16.7) – –

Irrigation, stock 2 0 (0) – –

Other 4 0 (0) – –

Unused 25 1 (4.0) – –

22 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
xxx

xxx

x

x

x

x

A

B

Number of detections / Number of wells

Total coliform

Escherichia coli

0

10

20

30

40

50

60

70

80

90

100

Domestic Public Irrigation,

stock

Other Unused

CLASS OF WATER USE

DETECTIONS OF COLIFORM BACTERIA, IN PERCENT

Commercial,

industrial,

institutional,

recreation

Domestic Public Commerical,

industrial,

institutional,

recreation

Irrigation, Other Unused

stock

1

10

100

1000

405 Number of values 

1.5 X interquartile

 range

1.5 X interquartile

 range

75th percentile

Median

25th percentile

Lower detached

Lower outside

Upper detached

Upper outside

Escherichia coli

EXPLANATION 

Total coliform

SCHEMATIC BOXPLOT

405 397 227 220 27 24 12 38 7 14 37 48

Minimum reporting level

Upper reporting level

waI9-0018_fig12 CONCENTRATION, IN COLONY-FORMING UNITS PER 100 MILLILITERS

8/37

1/7

3/12

9/27

36/227

134/405

31/397

6/220 1/24

3/38

4/14

9/48

x

x

Figure 12. Percentage of wells testing positive for coliform bacteria (A), and concentrations 

of coliform bacteria by class of water use (B) in samples collected in major aquifer study 

(MAS) and source-water quality assessment (SWQA) wells in 22 study units of the National 

Water-Quality Assessment program, 1993–2004.

Microbial Quality of Water in Principal Aquifers 23
Coliphage Viruses and Water Supplies

Samples for wells completed in 10 principal aquifers 

were analyzed for the presence of coliphage (table 8). 

Wells in 9 of these 10 aquifers were sampled as part of the 

MAS networks and wells in 7 of the aquifers were sampled 

as part of the SWQA networks. In 4 aquifers (Floridan, 

Central Valley, Coastal Lowlands, and Columbia Plateau), 

from 2 to 6 wells tested positive for coliphage (fig. 7A and 

B). Although no coliphages were detected in public-supply 

wells sampled in the Coastal Lowlands aquifer, coliphages 

were detected in 3 of 24 public-supply wells in the Floridan 

aquifer, in 1 of 15 public-supply wells in the Central Valley 

aquifer, and in 1 of 34 public-supply wells in the Columbia 

Plateau aquifer. A few domestic wells also tested positive 

for coliphage, but the frequency of detection was less than 

4 percent. Only 7 of all 200 domestic wells and 5 of all 183 

(less than 3 percent) public-supply wells sampled tested 

positive for coliphage (table 7).

The presence or absence of coliphage viruses in samples 

did not show any relation to concentrations of total coliforms 

or E. coli. Specifically, coliphage could be present with total 

coliforms at low concentrations of 1 CFU/100mL or less 

(undetected), or they could be absent from samples when 

total-coliform concentrations were as high as 100 CFU/100mL 

(fig. 13). Only one of the coliphage-positive samples also 

tested positive for E. coli. This lack of co-occurrence of 

bacteria and coliphage is consistent with the understanding 

that no single organism can fully function as an indicator for 

the presence of different types of microorganisms (Cabelli, 

1978; Havelaar and others, 1993). In a study of small publicsupply systems, Francy and others (2004) also determined a 

lack of co-occurrence between concentrations or detections of 

coliform bacteria and coliphage.

Occurrence of Coliform Bacteria and Relation 

to Well Depth and Selected Water-Quality 

Characteristics

The Kruskal-Wallis test indicated that one or more 

groups of well depths within study networks, uses of water, 

principal aquifers, and lithology differed (p-values <0.05) in 

their medians or distribution of values. Wells in the SWQA 

and MAS networks with median depths of 400 feet and 

150 feet below land surface, respectively, were significantly 

deeper than wells of the LUS networks (median depth of about 

50 feet below land surface), and public-supply wells (median 

depth of 427 feet) were deeper than wells used for domestic 

supply (median depth of 161 feet) or other purposes (fig. 14). 

For all 16 principal aquifers, the deepest wells sampled, with a 

median depth of 400 feet below land surface, were those in the 

Basin and Range aquifer (fig. 15). The depths of the publicsupply wells in the SWQA network and the wells in the Basin 

and Range aquifer might explain, in part, the relatively low 

detection frequencies of the coliform bacteria in these wells. 

A thick unsaturated zone increases the potential for natural 

attenuation of microorganisms, thereby reducing the potential 

for or preventing the bacteria being transported into the ground 

water.

Table 8. Summary of coliphage data collected from major 

aquifer study and source-water quality assessment wells in 

each principal aquifer studied by the National Water-Quality 

Assessment program, 1993–2004.

[Abbreviations: –, no data or not applicable]

Principal aquifer Number 

of wells

Number of wells 

with detections

(percentage)

Floridan 60 6 (10.0)

Central Valley 42 3 (7.1)

Coastal Lowlands 43 3 (7.0)

Columbia Plateau 36 2 (5.6)

Piedmont and Blue Ridge 12 0 (0)

Basin and Range 61 0 (0)

Glacial Deposits 66 0 (0)

High Plains 57 0 (0)

Mississippi Embayment-Texas Coastal 

Uplands

19 0 (0)

North Atlantic Coastal Plain 24 0 (0)

Ordovician (lower Tennessee) 0 –

Valley and Ridge 0 –

Mississippian-Pennsylvanian 0 –

Southeastern Coastal Plain 0 –

Stream and River Valley Alluvial 0 –

Snake River 0 –

24 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
Figure 13. Relation of the presence or absence of coliphage virus to concentrations of total coliforms for wells in 

the major aquifer study (MAS) networks and source-water quality assessment (SWQA) networks, and for principal 

aquifers with coliphage-positive wells.

waI9-0018_fig13

EXPLANATION

Sample from well in the Major Aquifer Study (MAS) Network

Sample from well in the Source-Water Quality Assessment (SWQA) Network

Columbia Plateau Aquifer,

Volcanic rocks

0.1 1 10 100

Floridan Aquifer,

Carbonate rocks

0.1 1 10 100

Central Valley Aquifer,

Sand, Gravel

0.1 1 10 100

TOTAL COLIFORMS, IN COLONY-FORMING

UNITS PER 100 MILLILITERS 

Coastal Lowlands Aquifer,

Sand, Gravel 

0.1 1 10 100

TOTAL COLIFORMS, IN COLONY-FORMING

UNITS PER 100 MILLILITERS

All samples from wells in the 

Major Aquifer Studies

0.1 1 10 100

Coliphage

present

Coliphage

absent

Coliphage

present

Coliphage

absent

All samples from wells in the SourceWater Quality Assessment

0.1 1 10 100

Coliphage

present

Coliphage

absent

Microbial Quality of Water in Principal Aquifers 25
waI9-0018_fig14

Major

aquifer

study

(MAS)

Land

use

study

(LUS)

Source-water

quality

assessment

(SWQA)

Domestic Public Commercial,

industrial,

institutional,

recreation

Irrigation,

stock

Other Unused

STUDY NETWORK CLASSES OF WATER USE

0

500

1000

1500

2000

2500

DEPTH OF WELL, IN FEET BELOW LAND SURFACE

75th percentile

Median

25th percentile

Upper outlier

Notch is 95-percent

 confidence interval

 about the median

1.5 X interquartile

 range

1.5 X interquartile

 range

EXPLANATION 

SCHEMATIC BOXPLOT

Figure 14. Distributions of well depths for the major aquifer study (MAS), land use study (LUS), and 

source-water quality assessment (SWQA) networks, and distribution of well depths for the classes of 

water use, from data collected in 22 study units of the National Water-Quality Assessment program, 

1993–2004.

26  Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
The principal aquifers were combined on the basis of 

median depths of sampled wells into three groups—shallow 

(median depths <100 feet), medium (median depths from 100 

to 200 feet), and deep (median depths greater than 200 feet) 

to identify any relations between well depth and detection 

frequencies or concentrations of total coliform bacteria 

(fig. 16). Of a total of 317 detections of total coliform bacteria, 

91 percent of the detections occurred in principal aquifers 

with median depths of sampled wells 200 feet deep or less, 

whereas only 9 percent of the detections occurred in the group 

of principal aquifers with median depths of sampled wells 

greater than 200 feet. The highest frequency of detection 

(50 percent) was in samples from wells in the medium group 

of aquifers with median well depths ranging from 100 to 200 

feet (fig. 16).

For wells in which total coliform bacteria were detected, 

concentrations in wells in the deep group of principal 

aquifers were lower (p-value <0.05) than concentrations in 

wells in the shallow and medium groups of aquifers. The 

graphs of the data (fig. 16) also illustrate the poor relation 

between total coliform bacteria concentration and well depth, 

which indicates that other factors are likely controlling the 

occurrence and transport of coliform bacteria in the aquifers. 

Some of these other factors might be the geohydrologic 

characteristics of the aquifers (fractured and porous rock 

types), proximity of contaminating sources such as septic 

tanks (Francy and others, 2000), or age of the well (Bickford 

and others, 1996), along with other well-construction features.

Shallow group Medium group Deep group

waI9-0018_fig15

10

100

1000

5

50

500

5000

DEPTH, IN FEET BELOW LAND SURFACE

Valley and Ridge

MississippianPennsylvanian

Glacial Deposits

Floridan

North Atlantic

Piedmont and Blue Ridge

Coastal Plain 

Mississippi Embayment-

 Texas Coastal Uplands

Central Valley

Stream and

River Valley

Southeastern

Coastal Plain

Coastal Lowlands

Columbia Plateau

High Plains

Basin and Range

Ordovician

(lower Tennessee)

Snake River

PRINCIPAL AQUIFER

1.5 X interquartile

 range

1.5 X interquartile

 range

75th percentile

Median

25th percentile

Upper outlier

EXPLANATION 

Figure 15. Distribution of well depths in the 16 principal aquifers studied by the National Water-Quality 

Assessment program, 1993–2004.

Microbial Quality of Water in Principal Aquifers 27
waI9-0018_fig16

DEPTH OF WELL, IN FEET BELOW LAND SURFACE

TOTAL-COLIFORM CONCENTRATION, IN COLONY-FORMING UNITS PER 100 MILLILITERS

0 1000 2000 3000

0 1000 2000 3000

0 200 400 600 800

0 200 400 600 800

1

10

100

1000

2

3

5

20

30

50

200

300

500

2000

1

10

100

1000

2

3

5

20

30

50

200

300

500

2000

All wells, all aquifers

967 samples

317 detections

33 percent detection frequency

393 samples

196 detections

50 percent detection frequency

398 samples

 94 detections

24 percent detection frequency

Shallow group of principal-aquifers,

median depth of sampled wells

less than 100 feet

Medium group of principal-aquifers,

median depth of sampled wells

100-200 feet

176 samples

27 detections

15 percent detection frequency

Deep group of principal-aquifers,

median depth of sampled wells

greater than 200 feet

Figure 16. Total-coliform concentrations and depths of wells for all 16 principal aquifers combined on the basis of the

median depths of sampled wells, from data collected in 22 study units of the National Water-Quality Assessment 

program, 1993-2004.

Figure 16. Total-coliform concentrations and depths of wells for all 16 principal aquifers combined on the basis of the 

median depths of sampled wells, from data collected in 22 study units of the National Water-Quality Assessment program, 

1993–2004.

The concentrations of selected chemical constituents 

(nutrients, major ions, dissolved oxygen, iron, manganese) 

and the measures of physical properties (specific conductance, 

water temperature) for samples collected from wells in the 

three major study networks also were evaluated for any 

relations to detections of total-coliform bacteria. There were 

significant differences (at the 95-percent confidence level) 

between median numbers of detections and nondetections 

of total coliforms with concentrations of dissolved oxygen, 

nitrite-plus-nitrate nitrogen, and orthophosphate (fig. 17). 

However, as with well depths, no strong correlation could 

be identified between the detection or nondetection of 

total-coliform bacteria in a water sample and the values of 

water-quality constituents.

28  Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
Figure 17. Detections of total-coliform bacteria with concentrations of dissolved oxygen, nitrite-plusnitrate nitrogen, and orthophosphate in samples collected from wells in 22 study units of the National 

Water-Quality Assessment program, 1993–2004.

waI9-0018_fig17

.01 .05 .1 .5 1 5 10 50

.001 .005 .01 .05 .1 .5 1 5

0 5 10 15

NO DETECTION

DETECTION

NO DETECTION

TOTAL COLIFORM BACTERIA

DETECTION

NO DETECTION

DETECTION

DISSOLVED OXYGEN, IN MILLIGRAMS PER LITER

NITRITE-PLUS-NITRATE NITROGEN, IN MILLIGRAMS PER LITER

ORTHOPHOSPHATE, IN MILLIGRAMS PER LITER

1.5 X interquartile

 range

75th percentile

median

25th percentile

upper detached

1.5 X interquartile

 range

Notch is 95-percent confidence

interval about the median

EXPLANATION 

SCHEMATIC BOXPLOT

Discussion

Three objectives governed this analysis of the 

microbiological quality of the Nation’s ground water. First, 

to describe the spatial distribution and occurrence of selected 

fecal-indicator microorganisms in ground water on the basis 

of data collected for the NAWQA program from 1993 to early 

2004. In addition, to determine how well the 19 principal 

aquifers that are the focus of the NAWQA Cycle II program 

are represented by the data and determine whether gaps 

are in the data on a regional basis. Second, to describe how 

fecal-indicator bacteria and coliphage are distributed within 

the aquifers by evaluating how microbial concentrations 

or detection frequencies relate to well depths, to types of 

aquifer materials, or to selected water-quality constituents 

or properties. Third, to identify what types and at what 

frequencies the fecal-indicator bacteria and coliphage are 

detected in water of the principal aquifers or in water used for 

drinking-water supplies.

Discussion 29
The set of microbiological data collected for the NAWQA 

program provided a relatively large number of observations 

with which to describe, in a general way, the geographic 

distribution and occurrence of fecal-indicator bacteria and 

coliphage in ground-water resources across the Nation. The 

data showed that wells testing positive for coliform bacteria 

exist within each study unit in which microbiological data 

were collected, with the highest frequencies of detections 

in wells in the northeastern and southeastern regions of 

the country and the fewest in the Idaho Upper Snake River 

and Nevada Basin and Range study areas. However, at the 

time of this analysis, fecal-indicator bacteria data had been 

collected in only 22 of the 50 NAWQA study units, and these 

data represented 12 of the 19 principal aquifers targeted by 

NAWQA in Cycle II. Additionally, data on the presence or 

absence of the coliphage viruses were collected in 11 of the 

22 study units. Gaps in the data, therefore, included more 

than 20 study units and 7 principal aquifers for which fecalindicator bacteria data were unavailable and more than 

30 study units for which coliphage data were unavailable for 

this analysis.

The Glacial Deposits, the Valley and Ridge, and 

the Piedmont and Blue Ridge aquifers had the greatest 

representation in the data, with a total of more than 420 

analytical results for the fecal-indicator bacteria; no data, 

however, were available for the New England, EdwardsTrinity, California Coastal Basins, Biscayne, and CambrianOrdovician aquifers, or the Surficial aquifer systems of 

the Southeast. Aquifers that might be geographically 

underrepresented by this data set include the High Plains, 

except for the northernmost part; that part of the Basin and 

Range aquifer in Arizona and southern California; and the 

Denver Basin. Also geographically underrepresented are the 

Midwest regions and the greater Mississippi River Basin.

Another type of geographic underrepresentation would 

apply to the Glacial Deposits, North Atlantic Coastal Plain, 

Piedmont and Blue Ridge, and Coastal Lowlands principal 

aquifers. Although the data set contains relatively large 

numbers of results for these aquifers, the sampled wells are 

clustered in small, isolated areas and leave extensive areas of 

the aquifer without representation. The clustering is likely due 

to geographic boundaries of study units and to the types of 

well networks established for the NAWQA program, which 

dictated certain locations with suitable wells for meeting 

network study objectives.

Eleven of the 42 study units scheduled for inclusion in 

Cycle II are represented in this analysis. The advantages of 

microbiological data collected as part of Cycle II is a data set 

consisting of common analytical methods, target organisms, 

and quality assurance-quality control procedures. Forthcoming 

Cycle II data will help to fill some of the spatial gaps and 

greatly enhance the information on the occurrence of the 

coliphage viruses, for which testing only recently became 

part of regularly scheduled analyses for the well networks. 

These additional data should prove valuable for a more 

comprehensive understanding of the quality of source waters 

for drinking-water supplies than described in this report.

The data showed general tendencies for detection 

frequencies and concentrations of total coliform bacteria to 

be higher (1) in principal aquifers with median well depths 

less than 200 feet than in principal aquifers with median 

well depths greater than 200 feet; (2) in domestic wells 

than in public-supply wells; and (3) in wells completed in 

fractured rocks or porous carbonate rocks than in sand, gravel, 

semiconsolidated sand, and volcanic rocks. Evaluations of the 

additional water-quality data (analyses for major chemical 

constituents) also showed tendencies for higher rates of 

total coliform detections with increasing concentrations of 

nitrite-plus-nitrate nitrogen and dissolved oxygen. With no 

strong correlations, however, the presence or absence of 

coliform bacteria cannot be predicted on the basis of well 

depth, lithology, or water chemistry, a situation that has been 

historically documented (Pipes, 1978, p. 106) and shown 

more recently in NAWQA studies by Bickford and others 

(1996) and Francy and others (2000). The data collected for 

the NAWQA program during 1993-2004 also showed that 

coliform bacteria tend to occur relatively frequently in ground 

water, with nearly 30 percent of the wells testing positive for 

these bacteria. Even though some of the members of the total 

coliform group originate from nonfecal sources, they can still 

function as conservative indicators of the potential for other 

microorganisms to enter the ground water. Conversely, E. coli

and coliphage viruses indicate contamination from fecal and 

sewage sources, which could be a more serious situation with 

respect to potential presence of pathogenic microorganisms 

and human health. Fortunately, E. coli and coliphage 

were detected in ground water at much lower frequencies 

(11 percent and 3 percent, respectively) than the total-coliform 

bacteria.

This analysis provided insight into the quality of the 

ground water used for drinking-water supplies by revealing 

the large numbers of domestic wells affected by the presence 

of coliform bacteria. Total-coliform bacteria were detected 

in samples from 33 percent of 405 domestic wells and 

16 percent of 227 public supply wells. No USEPA criteria or 

standards govern the acceptability of private-well water, and 

no routine monitoring is required for domestic supplies as 

for public supplies (U.S. Environmental Protection Agency, 

2005). A study of ground water in California determined 

that about one-fourth of the privately owned wells used for 

domestic supply in a two-county study area had some level of 

contamination by fecal-indicator bacteria (Bowman, 2005). 

In response to that determination, the California State Water 

Resources Control Board suggested that the detections of 

bacteria and other contaminants might warrant a program of 

testing by homeowners at a proposed frequency of every 5 

years (Bowman, 2005). The USEPA, recognizing that about 

15 percent of the population relies on private drinking-water 

30 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
supplies, provides Internet-based educational materials and 

also recommends that these households take precautions to 

protect and maintain their systems in addition to obtaining 

periodic testing by a certified laboratory (U.S. Environmental 

Protection Agency, 2005).

The data collected for the NAWQA program and the 

summary of the microbial quality of ground water in this 

report provide a basic understanding and current description of 

occurrence and relatively widespread distribution of coliform 

bacteria. The results presented here can serve as a starting 

point for continued assessments of the microbial quality of 

water in the principal aquifers of the United States as the 

NAWQA data set expands and perhaps also serve as a basis 

for water and public-health managers concerned with groundwater resources at the local level, particularly those used for 

domestic purposes.

Summary

Microbiological data were collected from 1,205 wells 

in 22 study units of the National Water-Quality Assessment 

(NAWQA) program during 1993 to 2004, a period spanning 

the first decade (Cycle I) and the early part of the second 

decade (Cycle II) of the program. The samples of untreated 

ground water were analyzed primarily for concentrations 

of total-coliform bacteria, fecal-coliform bacteria, and 

Escherichia coli (E. coli), and for the presence of coliphage 

viruses. Water temperature, pH, specific conductance, and 

dissolved-oxygen concentrations were measured at the time 

of sampling for microorganisms, and water samples were 

collected for analysis of a broad suite of chemical constituents, 

including nutrients.

The wells sampled for this analysis were part of 

NAWQA’s specific study networks: those for the major-aquifer 

studies (MAS) and land-use (LUS) studies, and the wells 

sampled for the source-water-quality assessments (SWQA) 

of ground water used for public supplies. The networks were 

situated within 16 principal aquifers.

For the purpose of this analysis, wells were assigned to 

one of seven types of principal-aquifer lithology (consolidated 

carbonate rocks; crystalline rocks; sandstone-shale rocks; 

semiconsolidated sand; unconsolidated sands, gravels, or 

alluvium; and volcanic rocks) on the basis of well completion 

information. Wells were also assigned to one of six classes of 

water use.

Nearly 30 percent of the 1,174 wells used in the study 

tested positive for coliform bacteria. With at least one well 

in each study unit or principal aquifer testing positive, fecalindicator bacteria were geographically widespread. Detection 

frequencies for bacteria in wells within individual study 

units ranged from 1 percent of sampled wells in the Upper 

Snake to 70 percent of wells in the Lower Susquehanna. 

Concentrations of total coliforms ranged from less than (<)1 to 

1,600 colony-forming units per 100 milliliters (CFU/100mL) 

and concentrations of E. coli ranged from <1 to 1,200 

CFU/100mL. Median concentrations for both total coliforms 

and E. coli, however, were at the reporting limit of <1 CFU/

100mL. Sixty-seven percent of total-coliform and 85 percent 

of E. coli concentrations were <100 CFU/100mL, indicating 

that overall, concentrations tend to be low.

In 11 of the 22 study units, samples were collected 

from 423 wells to test for the presence of coliphage viruses. 

Coliphage were present in samples from 4 of the 11 study 

units—the Central Columbia Plateau-Yakima , GeorgiaFlorida, San Joaquin, and Trinity, representing the Columbia 

Plateau, Floridan, Central Valley, and Coastal Lowlands 

aquifers, respectively.

Wells used for domestic supply made up the largest class 

of water use, with total-coliform concentrations for 405 wells 

and E. coli concentrations for 397 wells, followed by publicsupply wells and unused wells with 227 and 37 concentrations 

of total-coliform bacteria, respectively. Total coliforms were 

detected in untreated water from 33 percent of domestic 

wells and 16 percent of public-supply wells; E. coli were 

detected in 8 and 3 percent of domestic and public-supply 

wells, respectively. Although median concentrations were 

<1 CFU/100mL for all classes of water use as defined in this 

report, the overall distribution of total–coliform concentrations 

was significantly higher in domestic wells than in publicsupply wells. Coliphage were present in less than 4 percent of 

domestic and public wells used for drinking-water supply.

More than 50 percent of the wells sampled in the Valley 

and Ridge, the Floridan, and the Piedmont and Blue Ridge 

principal aquifers tested positive for coliform bacteria. 

Detection rates for the Floridan and the Piedmont and Blue 

Ridge aquifers were significantly higher than those for the 

Glacial Deposits, Stream and River Valley, Columbia Plateau, 

Basin and Range, High Plains, Southeastern Coastal Plain, and 

Coastal Lowlands aquifers. In 9 of the 16 aquifers, more than 

75 percent of the concentrations of total coliform and E. coli in 

samples were <1 CFU/100mL. The maximum concentrations 

of total coliform bacteria and of E. coli detected in all samples 

analyzed were from a domestic well completed in dolomite 

of the Valley and Ridge principal aquifer. The highest overall 

concentrations of total coliform bacteria were detected in this 

aquifer with a median of 2 CFU/100mL. High concentrations 

of coliform bacteria (greater than [>] 300 CFU/100mL) 

also were detected in samples from the MississippianPennsylvanian aquifer and the Ordovician aquifer in the lower 

Tennessee region.

Generally, coliform bacteria were detected more 

frequently and in higher concentrations in wells completed 

in sandstone or shale, and in sedimentary, carbonate, and 

crystalline rocks than for wells in unconsolidated materials, 

in semiconsolidated sand, or in volcanic rocks. More than 

Summary 31
50 percent of sampled wells completed in carbonate rocks 

(limestone, dolomite) or in crystalline rocks (schist, granite) 

tested positive for coliform bacteria. The Floridan, Piedmont 

and Blue Ridge, Ordovician, and Valley and Ridge aquifers, 

all of which had high detection rates or concentrations of 

coliform bacteria, are composed of these fractured and porous 

rocks. The lowest rates of detections (less than 5 percent) were 

for wells in the Basin and Range and Snake River aquifers. 

Materials in these aquifers are primarily unconsolidated sand, 

gravel, and clay, or basalt with interbeds of sand, gravel, or 

clay.

The depths of public-supply wells (median of 427 feet 

below land surface) and of the wells in the Basin and Range 

aquifer (median depth of 400 feet) might explain in part, the 

relatively low detection frequencies of the coliform bacteria 

observed in these samples. A thick unsaturated zone increases 

the potential for natural attenuation of microorganisms, 

preventing the bacteria being transported into the ground 

water. Fifty-percent of wells in principal aquifers with median 

depths of sampled wells ranging from 100 to 200 feet below 

land surface tested positive for total coliform bacteria, whereas 

only 9 percent of wells in principal aquifers with median 

depths of sampled wells greater than 200 feet tested positive. 

However, there were no strong correlations between well 

depth and coliform bacteria detections or concentrations that 

would predict the presence of coliform bacteria for any given 

well.

The data collected for the NAWQA program and the 

summary of the microbial quality of ground water in this 

report provide a current description of the occurrence and 

relatively widespread distribution of coliform bacteria in the 

Nation’s ground-water resources. The results presented here 

will serve as a starting point for continued assessments of the 

microbial quality of water in the principal aquifers.

Acknowledgments

The authors would like to thank Donna Francy and Don 

Stoeckel, Ohio Water Science Center of the USGS, for their 

guidance and advice during the data analysis. The helpful 

comments and suggestions for the report provided by USGS 

colleagues is greatly appreciated. Also, the authors gratefully 

acknowledge the assistance of Frank Voss, Washington Water 

Science Center of the USGS, for compiling GIS data layers 

and maps for illustrating principal aquifers and well networks 

of the NAWQA program; and Robert Black, Washington 

Water Science Center of the USGS, for technical assistance 

with statistical applications.

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34 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004
Manuscript approved for publication, November 14, 2006

Prepared by the USGS Publishing Network, 

Publishing Service Center, Tacoma, Washington

Bill Gibbs 

Bob Crist

Debra Grillo

Bobbie Jo Richey

Sharon Wahlstrom

Chet Zenone

For more information concerning the research in this report, contact the 

Director, Washington Water Science Center

U.S. Geological Survey, 934 Broadway — Suite 300

Tacoma, Washington 98402

http://wa.water.usgs.gov
Embrey and Runkle SIR 2006–5290 Microbial Quality of the Nation’s Ground-Water Resources, 1993–2004