U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Map 3234

National Water-Quality Assessment Program

Maps of Estimated Nitrate and Arsenic 

Concentrations for Basin-Fill Aquifers of the 

Southwestern United States
Cover art: Observed and predicted nitrate concentrations in basin-fill aquifers of the 

Southwest Principal Aquifers study area.
Maps of Estimated Nitrate and Arsenic 

Concentrations for Basin-Fill Aquifers 

of the Southwestern United States 

By Kimberly R. Beisner, David W. Anning, Angela P. Paul, Tim S. McKinney, 

Jena M. Huntington, Laura M. Bexfield, and Susan A. Thiros

National Water-Quality Assessment Program

Scientific Investigations Map 3234

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2012

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Suggested citation:

Beisner, K.R., Anning, D.W., Paul, A.P., McKinney, T.S., Huntington, J.M., Bexfield, L.M., and Thiros, S.A., 2012, Maps 

of estimated nitrate and arsenic concentrations in basin-fill aquifers of the southwestern United States: U.S. Geological Survey Scientific Investigations Map 3234, pamphlet 8 p., 2 sheets.
iii

Contents

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

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

Approach and Methods................................................................................................................................3

Classifier and Predicted Concentration Results.......................................................................................3

Classifier Goodness-of-Fit and Prediction Uncertainty.3

Nitrate ....................................................................................................................................................4

Arsenic....................................................................................................................................................7

Relevance and Implications.........................................................................................................................8

References Cited............................................................................................................................................8

Figures

1. Map showing the principal aquifers and locations of basins previously studied 

by the National Water-Quality Assessment Program in the Southwest Principal 

Aquifers study area ..................................................................................................................... 2

2. Bar graphs of statistical distribution of misclassification errors for the random 

forest prediction classifiers of basin-fill aquifers of the Southwest Principal 

Aquifers study area for nitrate and arsenic concentrations ............................................... 4

3. Pie charts showing percentage of nitrate concentration class for training 

observations and predictions .................................................................................................... 4

4. Pie charts showing percentage of arsenic concentration class for training 

observations and predictions .................................................................................................. 7

Plates

1. Observed and predicted nitrate concentrations in basin-fill aquifers of the Southwest 

Principal Aquifers study area. 

2. Observed and predicted arsenic concentrations in basin-fill aquifers of the Southwest 

Principal Aquifers study area. 

Tables

1. Relation between predicted nitrate and arsenic concentrations and explanatory 

variables representing conditions for basin-fill aquifers in the Southwest 

Principal Aquifers study area .................................................................................................... 5
iv

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

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).
Maps of Estimated Nitrate and Arsenic Concentrations for 

Basin-Fill Aquifers of the Southwestern United States

By Kimberly R. Beisner, David W. Anning, Angela P. Paul, Tim S. McKinney, Jena M. Huntington, Laura M. 

Bexfield, and Susan A. Thiros

Abstract

Human-health concerns and economic considerations 

associated with meeting drinking-water standards motivated 

a study of the vulnerability of basin-fill aquifers to nitrate 

contamination and arsenic enrichment in the southwestern 

United States. Statistical models were developed by using the 

random forest classifier algorithm to predict concentrations 

of nitrate and arsenic across a model grid representing about 

190,600 square miles of basin-fill aquifers in parts of Arizona, 

California, Colorado, Nevada, New Mexico, and Utah. The 

statistical models, referred to as classifiers, reflect natural 

and human-related factors that affect aquifer vulnerability to 

contamination and relate nitrate and arsenic concentrations 

to explanatory variables representing local- and basin-scale 

measures of source and aquifer susceptibility conditions. Geochemical variables were not used in concentration predictions 

because they were not available for the entire study area. The 

models were calibrated to assess model accuracy on the basis 

of measured values.

Only 2 percent of the area underlain by basin-fill aquifers 

in the study area was predicted to equal or exceed the U.S. 

Environmental Protection Agency drinking-water standard 

for nitrate as N (10 milligrams per liter), whereas 43 percent 

of the area was predicted to equal or exceed the standard for 

arsenic (10 micrograms per liter). Areas predicted to equal or 

exceed the drinking-water standard for nitrate include basins 

in central Arizona near Phoenix; the San Joaquin Valley, the 

Santa Ana Inland, and San Jacinto Basins of California; and 

the San Luis Valley of Colorado. Much of the area predicted 

to equal or exceed the drinking-water standard for arsenic is 

within a belt of basins along the western portion of the Basin 

and Range Physiographic Province that includes almost all of 

Nevada and parts of California and Arizona. Predicted nitrate 

and arsenic concentrations are substantially lower than the 

drinking-water standards in much of the study area—about 

93 percent of the area underlain by basin-fill aquifers was less 

than one-half the standard for nitrate as N (5.0 milligrams per 

liter), and 50 percent was less than one-half the standard for 

arsenic (5.0 micrograms per liter). The predicted concentrations and the improved understanding of the susceptibility 

and vulnerability of southwestern basin-fill aquifers to nitrate 

contamination and arsenic enrichment can be used by water 

managers as a qualitative tool to assess and protect the quality 

of groundwater resources in the Southwest.

Introduction

The National Water-Quality Assessment (NAWQA) 

Program of the U.S. Geological Survey (USGS) is performing a regional analysis of water quality in the principal aquifer 

systems across the United States (Lapham and others, 2005). 

The Southwest Principal Aquifers (SWPA) study is developing 

a better understanding of the susceptibility and vulnerability of 

basin-fill aquifers in the Southwest to groundwater contamination by synthesizing baseline knowledge of groundwater-quality conditions in 16 basins previously studied by the NAWQA 

Program (fig. 1). 

About 46.6 million people live in the SWPA study area 

(Oak Ridge National Laboratory, 2005), mostly in urban areas, 

but also in rural agricultural communities that cultivate about 

14.4 million acres of cropland (U.S. Geological Survey, 2003). 

Other rural areas contain small communities with mining, 

retirement, or tourism/recreational-based economies. Because 

of the generally limited availability of surface-water supplies 

in the arid to semiarid climate, cultural and economic activities in the region are dependent on high-quality groundwater 

supplies. In the year 2000, about 33.7 million acre-feet (acreft) of surface water was diverted from streams, and about 23.0 

million acre-ft of groundwater was withdrawn from basin-fill 

aquifers in the SWPA study area (U.S. Geological Survey, 

2004). Irrigation and public-supply groundwater withdrawals 

from basin-fill aquifers in the study area were about 18.0 million acre-ft and 4.1 million acre-ft, respectively, and together 

account for about one quarter of the total withdrawals from all 

aquifers in the United States (Maupin and Barber, 2005). 

Basin-fill aquifers underlie about half (190,600 square 

miles (mi2

)) of the 409,000 mi2 SWPA study area (fig. 1) and 

are the primary groundwater supply for most cities and agricultural communities. In several areas, these aquifers provide 

base flow to streams that support important aquatic and riparian habitats. Basin-fill aquifers primarily consist of sand and 

gravel deposits that partly fill faulted basins and are bounded 

by consolidated rock mountains. 
2 Maps of Estimated Nitrate and Arsenic Concentrations for Basin-Fill Aquifers of the Southwestern United States

Figure 1. The principal aquifers and locations of basins previously studied by the National Water-Quality Assessment Program in the 

Southwest Principal Aquifers study area.

WYOMING

Basin and Range basin-fill aquifers

California Coastal Basin aquifers

Central Valley aquifer system

Rio Grande aquifer system

Pacific Northwest basin-fill aquifers

Area without basin-fill aquifers

EXPLANATION

35°

Pacific Ocean

U.S. Geological Survey digital data, 1:500,000 and 750,000 scale, 1992–1997 and 2006

National Elevation Data 1:24,000 scale, 1999

Albers Equal Area Conic projection, NAD 83

40°

120° OREGON

115°

NEVADA

IDAHO

110°

Las Vegas

Valley

Salt River Valley—

Phoenix area

San Luis Valley

Salt Lake

Spanish Springs Valley Valley

Truckee River Basin—Reno/Sparks

Eagle Valley

Carson Valley

105°

CALIFORNIA

ARIZONA NEW MEXICO

UTAH COLORADO

0 50 100 150 200 Miles

0 50 100 150 200 Kilometers

MEXICO

Principal aquifers from U.S. Geological Survey, 2003

Sacramento

 Valley

San 

Joaquin

 Valley

Albuquerque-Belen 

Basin

Upper

San Pedro

Basin

Santa Ana Inland Basin 

San Jacinto Basin 

Upper

Santa Cruz

Basin

Santa Ana Coastal Basin 

Southwest 

Principal 

Aquifer (SWPA) 

study-area 

boundary

Similarities in the hydrogeology, land- and water-use practices, and water-quality issues allow for regional analysis of 

the vulnerability of basin-fill aquifers to contamination in the 

SWPA study area. Published studies have summarized current 

knowledge about the water quality of groundwater systems 

of basin-fill aquifers in the 16 basins previously studied by 

NAWQA (Thiros and others, 2010) and developed conceptual 

models of the primary natural and human-related factors commonly affecting groundwater quality in basin-fill aquifers on a 

regional scale (Bexfield and others, 2011). 

Nitrate and arsenic concentrations are known to be elevated in many areas of the west; however, the contributing factors are distinct for each constituent. The motivation for study 

of nitrate and arsenic concentrations in basin-fill aquifers in 

the SWPA study area arose from concerns about human-health 

issues and economic costs associated with the protection and 

treatment of drinking water with respect to these constituents, 

as well as the potential for contaminant concentrations to 

increase over time and degrade the quality of groundwater in 

the aquifers as development progresses.

The U.S. Environmental Protection Agency (USEPA) 

regulates nitrate in drinking water because of the potential 

for elevated nitrate to restrict oxygen transport in the blood 

of infants in a condition known as acquired methemoglobinemia or blue-baby syndrome (U.S. Environmental Protection 

Agency, 2012). Recent concern also has arisen over transformation of nitrate within the human body into N-nitroso 

compounds, which are known carcinogens (Ward and others, 

2005). The current nitrate as N standard of 10 milligrams per 

liter (mg/L) is the maximum allowable concentration of nitrate 

in drinking water delivered to the consumer by a public-supply 

system.

Arsenic has been recognized as a toxic element for centuries and is a human-health concern because elevated concentrations can contribute to a wide variety of adverse health 

effects, including skin damage and circulatory problems. In 

addition, arsenic in drinking water can lead to several types 
Classifier and Predicted Concentration Results 3

of cancers, including bladder, lung, skin, and possibly kidney 

and liver (National Research Council, 2001). On the basis of a 

review of available scientific research on health effects of arsenic, long-term consumption of drinking water in excess of 5 

micrograms per liter (μg/L) has been linked with an increased 

human-health risk (National Research Council, 2001). In light 

of the risk level, the USEPA lowered the drinking-water standard for arsenic from 50 μg/L to 10 μg/L, effective in 2006, as 

a compromise between the risk to individuals and the expense 

to water suppliers (U.S. Environmental Protection Agency, 

2012). 

This report summarizes statistical models developed by 

Anning and others (2012) that relate concentrations of nitrate 

and arsenic in basin-fill aquifers of the SWPA study area 

to selected natural and human-related factors representing 

contaminant sources and aquifer susceptibility conditions. 

Statistical models allow the understanding of nitrate and arsenic concentrations to be expanded from discrete observations 

to broader spatial predictions. Specifically, this report presents 

the spatial and statistical distribution of nitrate (plate 1) and 

arsenic (plate 2) concentrations in basin-fill aquifers across 

the SWPA study area as determined by using predictions from 

statistical models. 

Approach and Methods

Statistical models used in this investigation were constructed by using the random forest classifier algorithm 

(Breiman, 2001) and are hereafter called ‘classifiers.’ In 

short, the classifiers “learn” the relations between known 

nitrate and arsenic concentrations and known environmental 

conditions associated with the aquifer. These relations take 

the form of complex decision trees and are used with known 

spatially-distributed environmental-condition data to predict 

concentrations in areas where observed concentration data are 

unavailable. 

The concentration data used for training the classifiers 

were from 6,234 well samples stored in the USGS National 

Water Information System (NWIS; U.S. Geological Survey, 

2010). These data were partitioned into six concentration 

groups for nitrate and seven concentration groups for arsenic. 

The break points between concentration classes were 0.50, 1.0, 

2.0, 5.0, and 10 mg/L for nitrate and 1.0, 2.0, 3.0, 5.0, 10, and 

25 μg/L for arsenic. The environmental conditions represented 

in the classifiers were from several existing geospatial datasets 

and included factors such as nitrogen loading rates, geologic 

characteristics, soil conditions, land use, water use, and other 

hydrologic conditions. Anning and others (2012) developed 

exploratory models with geochemical conditions that were 

found not to greatly improve the accuracy of the predictions. 

The environmental factors considered in the statistical model 

are related to geochemical conditions and likely account for 

much of the variability without the need for direct use of 

geochemical data. Additionally, geochemical data were not 

available for the entire study area.

Classifier and Predicted Concentration 

Results

The random forest classifiers provided a context to evaluate the spatial distribution of nitrate and arsenic within the 

upper 200 ft of basin-fill aquifers in the study area and to 

assess the vulnerability of aquifers throughout the SWPA 

study area to nitrate contamination and arsenic enrichment. 

Predicted nitrate and arsenic concentrations are discussed in 

this report for the upper 200 ft of the aquifer primarily because 

regression analysis on observed data showed that, at the 

regional scale, systematic concentration variations with depth 

were not found in the aquifers. 

The classifiers were successfully trained to relations 

between observed nitrate and arsenic concentrations and 

important factors affecting them. This enabled the extrapolation of predicted nitrate and arsenic concentrations from areas 

where concentrations were measured into areas where data 

were unavailable. The nitrate and arsenic classifiers were 

found to be generally consistent with, and provided additional 

information and detail for, the conceptual models for natural and human-related factors affecting these constituents as 

described in Bexfield and others (2011). 

Classifier Goodness-of-Fit and Prediction 

Uncertainty

The classifiers for nitrate and for arsenic performed well 

for assessing the vulnerability of basin-fill aquifers in the 

SWPA study area to contamination by these constituents. 

The classifiers generally produced unbiased predictions, and 

misclassification errors for each classifier were generally low, 

given the spatial variability within individual model grid cells. 

For each explanatory variable, the range of values in the study 

area was well represented by nitrate and arsenic observations, 

and there were no environmental conditions poorly represented by the dataset used to train the classifiers. In addition, 

analysis of the misclassification errors indicated that there 

were no environmental conditions where the classifier tended 

to overpredict or underpredict concentrations. Analysis of the 

misclassifications indicated that the models were unbiased 

spatially and unbiased across the distribution of values for the 

explanatory variables. 

The ability of the model to predict concentrations across 

the study area within plus or minus one concentration class 

was 72 percent for nitrate and 70 percent for arsenic. Misclassification errors were generally symmetric about the correct 

(true) class; 29 percent of nitrate and 34 percent of arsenic 

observations were misclassified into lower concentration 

classes than the true class, and 29 percent of nitrate and 31 

percent of arsenic observations were misclassified into higher 

concentration classes (fig. 2).
4 Maps of Estimated Nitrate and Arsenic Concentrations for Basin-Fill Aquifers of the Southwestern United States

Nitrate

While the training observations indicate nitrate concentrations were equal to or exceeded 10 mg/L in 11 percent of 

the groundwater samples, use of the prediction classifier to 

extrapolate concentrations across the SWPA study area (plate 

1) revealed that only about 2 percent of the study area underlain by basin-fill aquifers is likely to exceed this concentration, 

and 93 percent of the area could have groundwater with less 

than 5.0 mg/L of nitrate as N (fig. 3). These differences in the 

distribution of observed and predicted nitrate concentrations 

are expected and result from the fact that the prediction dataset 

represents the full extent of basin-fill aquifers in the SWPA 

study area, whereas the training dataset represents a subset 

of those aquifers where observations were available. Generally, samples of groundwater were collected from areas where 

groundwater resources have been developed. The measured 

and predicted concentration datasets have somewhat different 

but overlapping distributions of source and aquifer-susceptibility variables that affect nitrate in groundwater. 

Relative background concentrations of nitrate in groundwater in undeveloped land-use settings were determined to 

be less than 2.0 mg/L for most biotic communities overlaying basin-fill aquifers, except for the Semidesert Grassland, 

Mojave Desertscrub, Sonoran Desertscrub-Arizona Uplands, 

and Sonoran Desertscrub-Lower Colorado River Valley communities generally located in southern Arizona. In these four 

biotic communities, concentrations were estimated to be less 

than 5.0 mg/L but greater than 2.0 mg/L. Nitrate concentrations greater than these relative background concentrations 

are largely found in areas with agricultural or urban land 

development. 

Concentrations of nitrate in the basin-fill aquifers were predicted to exceed relative background concentrations in about 

34 percent of areas having more than 5-percent agricultural or 

urban land. Exceedance of relative background concentrations 

increased with the amount of agricultural or urban development. Nitrate concentrations in basin-fill aquifers underlying 

land where greater than half the area has been developed for 

agricultural or urban uses are predicted to equal or exceed 10 

Figure 2. Statistical distribution of misclassification errors for 

the random forest prediction classifiers of basin-fill aquifers of the 

Southwest Principal Aquifers study area for nitrate and arsenic 

concentrations.

0

10

20

30

40

50

0

10

20

30

40

50

Percentage of training observations

Nitrate

Misclassification error, observed minus predicted class

-5 -4 -3 -2 -1 0 1 2 3 4 5

Correct,

42.3 pecent

Overpredicted, 29.0 percent Underpredicted, 28.7 percent

Arsenic

-5-6 -4 -3 -2 -1 0 1 2 3 4 5 6

Correct,

Overpredicted, 31.4 percent 34.4 percent Underpredicted, 34.2 percent

Predictions

Training observations

5%

2%

<0.50 mg/L

0.50 to 0.99 mg/L

1.0 to 1.9 mg/L

2.0 to 4.9 mg/L

5.0 to 9.9 mg/L

≥10 mg/L

42%

11%

28%

12%

<0.50 mg/L

0.50 to 0.99 mg/L

1.0 to 1.9 mg/L

2.0 to 4.9 mg/L

5.0 to 9.9 mg/L

≥10 mg/L

Nitrate

30%

11%

20%

16 %

12%

11%

Percentage of nitrate concentration class

[<, less than; ≥, equal to or greater than; mg/L, milligrams per liter; %, percent]

Figure 3. Percentage of nitrate concentration class for training 

observations and predictions.
Classifier and Predicted Concentration Results 5

mg/L in 15 percent of that area, which increases to 48 percent for areas entirely used for agricultural or urban related 

activities. Predicted concentrations generally decreased along 

groundwater-flow paths from the basin margin to the basin 

lowlands. Nearly all wetland areas in the basin lowlands have 

concentrations less than 0.50 mg/L, regardless of the amount 

of land development. These low concentrations could result 

from denitrification, a microbially facilitated process where 

nitrate is converted to nitrogen gas, although other explanations are possible (Anning and others, 2012). 

A further understanding of conditions that render the 

basin-fill aquifers in the SWPA study area vulnerable to nitrate 

contamination was gained from an analysis of the correlations 

between the predicted concentrations and the explanatory 

variables (table 1), as well as correlations between observed 

nitrate and other constituent concentrations in the training 

dataset, which are described in detail in Anning and others 

(2012). These univariate correlations indicated that areas are 

more likely to have higher concentrations and, therefore, are 

generally more vulnerable to nitrate contamination, where one 

or more of the following conditions is found:

• Land is used for agricultural or urban purposes, especially where fertilizers are used or where there are 

livestock.

[Positive values of Kendall’s tau indicate that higher concentrations are associated with greater values of the explanatory variable and lower concentrations are associated with lesser 

values of the explanatory variable. Negative values of Kendall’s tau indicate that the opposite relation exists between concentration and the explanatory variable. Small p-values 

(<0.001) indicate the Kendall’s tau correlation between the nitrate or arsenic concentration and a given explanatory variable is statistically significant. Abbreviations: —, constituent 

not tested in classifier; <, less than]

Variable 

group Explanatory variable Represented area

Kendall’s tau test on predicted 

nitrate concentration

Kendall’s tau test on predicted 

arsenic concentration

tau p-value tau p-value

Source variables

Nitrogen loading

Atmospheric deposition Grid cell –0.06 <0.001 — —

Farm fertilizer Grid cell 0.06 <0.001 — —

Non-farm fertilizer Grid cell 0.05 <0.001 — —

Confined manure Grid cell 0.06 <0.001 — —

Unconfined manure Grid cell 0.03 <0.001 — —

Total nitrogen Grid cell 0.01 <0.001 — —

Land use

Septic/sewer ratio Grid cell –0.02 <0.001 –0.07 <0.001

Local population Grid cell 0.09 <0.001 –0.16 <0.001

Local population density Grid cell 0.09 <0.001 –0.16 <0.001

Basin population Basin average 0.08 <0.001 –0.18 <0.001

Basin population density Basin average 0.10 <0.001 –0.20 <0.001

Local urban land Grid cell 0.08 <0.001 –0.15 <0.001

Local agricultural land Grid cell 0.04 <0.001 –0.11 <0.001

Basin urban land Basin average 0.08 <0.001 –0.21 <0.001

Basin agricultural land Basin average 0.02 <0.001 –0.20 <0.001

Basin rangeland Basin average 0.00 0.551 0.29 <0.001

Basin other land cover Basin average –0.11 <0.001 –0.26 <0.001

Geologic sources

Carbonate rocks Contributing area -0.15 <0.001 –0.07 <0.001

Crystalline rocks Contributing area 0.18 <0.001 0.04 <0.001

Clastic sedimentary rocks Contributing area –0.10 <0.001 –0.16 <0.001

Mafic volcanic rocks Contributing area 0.08 <0.001 0.16 <0.001

Felsic and silicic volcanic rocks Contributing area –0.11 <0.001 0.04 <0.001

Intermediate composition volcanic rocks Contributing area 0.05 <0.001 0.11 <0.001

Undifferentiated volcanic rocks Contributing area 0.00 0.855 –0.07 <0.001

Distance to carbonate rocks Grid cell 0.11 <0.001 0.07 <0.001

Distance to crystalline rocks Grid cell –0.11 <0.001 –0.02 <0.001

Distantce to clastic sedimentary rocks Grid cell 0.03 <0.001 0.14 <0.001

Distance to mafic volcanic rocks Grid cell –0.10 <0.001 –0.19 <0.001

Distance to felsic and silicic volcanic rocks Grid cell 0.07 <0.001 –0.06 <0.001

Distance to intermediate composition volcanic rocks Grid cell –0.02 <0.001 –0.12 <0.001

Distance to undifferentiated volcanic rocks Grid cell 0.01 0.006 0.03 <0.001

Soil and rock equivalent uranium-238 Grid cell — — 0.14 <0.001

Table 1. Relation between predicted nitrate and arsenic concentrations and explanatory variables representing conditions for basinfill aquifers in the Southwest Principal Aquifers study area.
6 Maps of Estimated Nitrate and Arsenic Concentrations for Basin-Fill Aquifers of the Southwestern United States

[Positive values of Kendall’s tau indicate that higher concentrations are associated with greater values of the explanatory variable and lower concentrations are associated with lesser 

values of the explanatory variable. Negative values of Kendall’s tau indicate that the opposite relation exists between concentration and the explanatory variable. Small p-values 

(<0.001) indicate the Kendall’s tau correlation between the nitrate or arsenic concentration and a given explanatory variable is statistically significant. Abbreviations: —, constituent 

not tested in classifier; <, less than]

Variable 

group Explanatory variable Represented area

Kendall’s tau test on predicted 

nitrate concentration

Kendall’s tau test on predicted 

arsenic concentration

tau p-value tau p-value

Aquifer susceptibility variables

Flow path

Land-surface slope Grid cell 0.05 <0.001 –0.12 <0.001

Land-surface elevation Grid cell –0.17 <0.001 –0.10 <0.001

Land-surface elevation percentile Grid cell 0.15 <0.001 –0.16 <0.001

Basin elevation Basin average –0.20 <0.001 –0.07 <0.001

Distance to basin margin Grid cell –0.02 <0.001 0.08 <0.001

Soil properties

Seasonally high water depth Grid cell 0.25 <0.001 –0.03 <0.001

Hydric Grid cell –0.22 <0.001 0.04 <0.001

Hydrologic group A1 Grid cell –0.13 <0.001 0.14 <0.001

Hydrologic group B2 Grid cell 0.20 <0.001 –0.04 <0.001

Hydrologic group C3 Grid cell –0.01 <0.001 –0.11 <0.001

Hydrologic group D4 Grid cell –0.20 <0.001 0.00 0.806

Permeability Grid cell –0.07 <0.001 0.16 <0.001

Organic material Grid cell 0.00 0.695 –0.15 <0.001

Clay Grid cell –0.02 <0.001 –0.07 <0.001

Silt Grid cell –0.13 <0.001 –0.09 <0.001

Sand Grid cell 0.12 <0.001 0.09 <0.001

Water use and hydroclimatic

Water-resources development index Basin average 0.04 <0.001 –0.20 <0.001

Groundwater use, irrigated agriculture Grid cell 0.05 <0.001 –0.11 <0.001

Surface-water use, irrigated agriculture Grid cell 0.04 <0.001 –0.11 <0.001

Groundwater use, public water supply Grid cell 0.03 <0.001 –0.06 <0.001

Surface-water use, public water supply Grid cell 0.03 <0.001 –0.05 <0.001

Recharge, contributing area Contributing area 0.00 0.938 –0.37 <0.001

Recharge, basin Basin average 0.02 <0.001 –0.37 <0.001

Potential evapotranspiration Grid cell 0.23 <0.001 0.13 <0.001

Mean air temperature Grid cell 0.23 <0.001 0.13 <0.001

1

 Hydrologic Group A—Sand, loamy sand, or sandy loam types of soils. Low runoff potential and high infiltration rates even when thoroughly wetted. Consists chiefly of deep, well to excessively drained sands or gravels and has a high rate of water transmission.

2

 Hydrologic Group B—Silt loam or loam types of soils. Moderate infiltration rate when thoroughly wetted and consists chiefly of moderately deep to deep, 

moderately well to well drained soils with moderately fine to moderately coarse textures.

3

 Hydrologic Group C—Sandy clay loam type of soil. Low infiltration rates when thoroughly wetted and consists chiefly of soils with a layer that impedes 

downward movement of water and soils with moderately fine to fine structure.

4

 Hydrologic Group D—Clay loam, silty clay loam, sandy clay, silty clay, or clay types of soils. Highest runoff potential and very low infiltration rates when 

thoroughly wetted. Consists chiefly of clay soils with a high swelling potential, soils with a permanent high water table, soils with a claypan or clay layer at or 

near the surface, and shallow soils over nearly impervious material.

Table 1. Relation between predicted nitrate and arsenic concentrations and explanatory variables representing conditions 

for basin-fill aquifers in the Southwest Principal Aquifers study area.—Continued

• Nitrogen is fixed by natural vegetation, such as legumes 

in the Sonoran Desert.

• Soils are present that have textures favorable to water 

infiltration, lack hydric conditions, or lack organic 

material. 

• High water-use from groundwater or surface-water supplies for agricultural purposes or public-water supply.

• Natural recharge is low in the drainage area contributing 

flow to the groundwater basin.

• Mean air temperatures and potential evapotranspiration 

are high.

• Bedrock surrounding the basin-fill aquifer has an abundance of crystalline, mafic volcanic, and intermediate 

composition volcanic rock, which likely produces geochemical conditions favorable to nitrate persistence. 
Classifier and Predicted Concentration Results 7

Arsenic

While the training observations indicated arsenic concentrations equal or exceed 10 μg/L in 25 percent of the groundwater samples, use of the prediction classifier to extrapolate 

concentrations across the SWPA study area (plate 2) revealed 

43 percent of the area underlain by basin-fill aquifers is likely 

to exceed this concentration, whereas 50 percent of the area 

could have concentrations less than 5.0 μg/L (fig. 4). Such 

differences in the distributions of observed and predicted arsenic concentrations are expected and result from the fact that 

the prediction dataset represents the full extent of basin-fill 

aquifers in the SWPA study area, whereas the training dataset represents a subset of those aquifers where observations 

were available, and each dataset has somewhat different but 

overlapping distributions of source and aquifer-susceptibility 

variables that affect arsenic in groundwater. 

The largest area where arsenic concentrations in groundwater were predicted to be equal to or greater than the drinkingwater standard of 10 μg/L was in the Basin and Range basinfill aquifers (fig. 1, plate 2). Spatially, the Basin and Range 

basin-fill aquifers compose about 73 percent of the regional 

study area, and much of the area is undeveloped or used as 

open rangeland. Distribution patterns with depth obtained 

from the random forest classifiers support the conceptualmodel findings indicating that arsenic concentrations can 

exceed 10 μg/L at various depths within aquifers throughout 

the SWPA study area (Bexfield and others, 2011).

Within a given basin, predicted concentrations generally 

increased along groundwater-flow paths from the upper basin 

margins to the basin lowlands, with greater concentrations 

associated with basin-fill sediments derived from surrounding 

mountains predominately composed of volcanic or crystalline bedrock. Basins surrounded by carbonate rocks generally 

contained groundwater with lower predicted concentrations 

of arsenic. Although areas developed for agricultural or urban 

use had lower observed and predicted arsenic concentrations 

compared to minimally developed areas, this is thought to be 

largely an artifact of the hydrogeologic nature of the developed areas. Generally, the more developed areas have higher 

rates of natural recharge because of the availability of water 

resources and possibly greater flushing rates of solutes out of 

the basin either to rivers or the ocean. In contrast, basins with 

lower rates of natural recharge, and likely correspondingly 

lower flushing rates of solutes, tend to be less developed and 

generally located in areas with relatively high potential evapotranspiration rates.

A further understanding of conditions that render the basinfill aquifers in the SWPA study area vulnerable to arsenic 

enrichment was gained from an analysis of the correlations 

between the predicted concentrations and the explanatory 

variables (table 1), as well as correlations between observed 

arsenic and other constituent concentrations in the training 

dataset, which are described in detail in Anning and others 

(2012). These univariate correlations indicated that higher 

Predictions

Training observations

15%

13%

7%

11%

11%

26%

17%

13%

15%

17% 14%

16 %

14%

11%

Percentage of arsenic concentration class

[<, less than; ≥, equal to or greater than; μg/L, micrograms per liter; %, percent]

<1.0 μg/L

1.0 to 1.9 μg/L

2.0 to 2.9 μg/L

3.0 to 4.9 μg/L

5.0 to 9.9 μg/L

≥25 μg/L

10 to 24 μg/L

Arsenic

<1.0 μg/L

1.0 to 1.9 μg/L

2.0 to 2.9 μg/L

3.0 to 4.9 μg/L 5.0 to 9.9 μg/L

≥25 μg/L

10 to 24 μg/L

Figure 4. Percentage of arsenic concentration class for training 

observations and predictions.

arsenic concentrations are more likely to be found in areas 

where the following conditions exist:

• Basins are surrounded by mafic volcanic bedrock, felsic/

silicic volcanic bedrock, or crystalline bedrock.

• Long groundwater-flow paths.

• There is a general lack of groundwater flushing as 

indicated by low rates of natural recharge, high potential evapotranspiration rates, and minimal or altogether 

absent groundwater flow out of the basin.

• Geochemical conditions favor the release of arsenic from 

aquifer substrates to surrounding groundwater. 
8 Maps of Estimated Nitrate and Arsenic Concentrations for Basin-Fill Aquifers of the Southwestern United States

Relevance and Implications

Areas predicted to exceed the nitrate drinking-water 

standard are generally developed, especially for irrigated 

agriculture, but are also located in more urbanized locations 

such as Phoenix, Arizona, and Modesto and suburbs east 

of Los Angeles, California. While population densities are 

generally much lower in agricultural areas than in urban areas, 

high nitrate concentrations underlying agricultural landscapes 

could be problematic with respect to public supply for large 

populations if those lands are eventually converted to urban 

uses. For the areas affected by high nitrate concentrations in 

agricultural land-use settings, fertilizer and livestock manure 

are significant sources and are typically mitigated with best 

management practices. Large tracks of land in the Sonoran 

Desert with nitrate concentrations between 2.0 and 5.0 mg/L, 

however, appear to be affected by natural nitrogen fixation by 

legumes and present a more challenging condition for nitrogen 

management. 

Arsenic in groundwater is derived primarily from natural sources, namely the basin-fill sediments and the parent 

bedrock from which the sediments were derived. Whereas 

most of the area predicted to have arsenic concentrations equal 

to or greater than the current drinking-water standard of 10 

μg/L is sparsely populated, major population centers are not 

necessarily unaffected. Areas within or adjacent to the metropolitan areas of Albuquerque, Bakersfield, Phoenix, Reno, 

Sacramento, Salt Lake City, and Stockton have measured and 

predicted arsenic concentrations above the drinking-water 

standard, which could affect future groundwater development 

as these cities grow. 

As population centers in the west continue to grow, areas 

that are currently undeveloped are sought for alternative 

public-water supplies. Currently available groundwater data 

are generally focused on areas where wells already exist for 

groundwater development. The statistical model and associated reconnaissance scale maps of predictions (plates 1 and 2) 

for nitrate and arsenic concentrations are representative of the 

entire basin-fill groundwater resource available in the Southwest. The maps are based on statistical models that do not 

include geochemical data, and can help inform future management strategies as well as identify the need for additional 

locally relevant information in areas of interest.

References Cited

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Bexfield, L.M., and Thiros, S.A., 2012, Predicted nitrate 

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Beisner and others—Maps of Estimated Nitrate and Arsenic Concentrations for Basin-Fill Aquifers of the Southwestern United States—Scientific Investigations Map 3234

Printed on recycled paper

Southwest Principal Aquifers—Includes (from left to right) California Coastal Basin aquifers, Central 

Valley aquifer system, Basin and Range basin-fill aquifers, and Rio Grande aquifer system