U.S. Department of the Interior

U.S. Geological Survey

Open File 2008–1272

October 2008

Prepared in cooperation with Northeastern San Joaquin Groundwater Banking Authority and California Department of Water Resources

Source, Distribution, and Management of Arsenic in Water from 

Wells, Eastern San Joaquin Ground-Water Subbasin, California 

Printed on recycled paper

By John A. Izbicki, Christina L. Stamos, Loren F. Metzger, Keith J. Halford, Thomas R. Kulp, and George L. Bennett

5

5

Lodi

Manteca

Stockton

0 5 10 15 Kilometers

0 5 10 15 Miles

San

Joaquin

Delta

Mokelumne River

Stanislaus River

San Joaquin River

Less than 5

5 to 10

10 to 15

Greater than 15

Arsenic concentra-

 tion in water from

 wells, in micrograms

 per liter (1974-2001)

Eastern San Joaquin

 Ground-Water

 Subbasin

EXPLANATION

STUDY

AREA

Sierra Nevada

San

Francisco

Central

Valley

C

A

L I F

O

R

N I A

Pacific Ocean

Stockton

12J1

1A1-5

11H4-8

20N1

0 5 10 Kilometers

0 5 10 Miles

San Joaquin River

Multiple-well site

Well with depth-

 dependent data

5

Summary

Between 1974 and 2001 

water from as many as onethird of wells in the Eastern San 

Joaquin Ground-Water Subbasin, 

about 80 miles east of San Francisco, had arsenic concentrations 

greater than the U.S. Environmental Protection Agency Maximum 

Contaminant Level (MCL) for 

arsenic of 10 micrograms per liter 

(μg/L). Water from some wells 

had arsenic concentrations greater 

than 60 μg/L. The sources of 

arsenic in the study area include 

(1) weathering of arsenic bearing minerals, (2) desorption of 

arsenic associated with iron and 

manganese oxide coatings on the 

surfaces of mineral grains at pH’s 

greater than 7.6, and (3) release of 

arsenic through reductive dissolution of iron and manganese oxide 

coatings in the absence of oxygen. 

Reductive dissolution is responsible for arsenic concentrations 

greater than the MCL. The distribution of arsenic varied areally 

and with depth. Concentrations 

were lower near ground-water 

recharge areas along the foothills 

of the Sierra Nevada; whereas, 

concentrations were higher in 

deeper wells at the downgradient 

end of long flow paths near the 

margin of the San Joaquin Delta 

(fig. 1). Management opportunities to control high-arsenic 

concentrations are present because 

water from the surface discharge 

of wells is a mixture of water from 

the different depths penetrated by 

wells. On the basis of well-bore 

flow and depth-dependent waterquality data collected as part of 

this study, the screened interval of 

a public-supply well having arsenic concentrations that occasionally exceed the MCL was modified 

to reduce arsenic concentrations in 

the surface discharge of the well. 

Arsenic concentrations from the 

modified well were about 7 μg/L. 

Simulations of ground-water flow 

to the well showed that although 

upward movement of high-arsenic 

water from depth within the aquifer occurred, arsenic concentrations from the well are expected to 

remain below the MCL.

Figure 1. Arsenic concentrations in water from wells (1974-2001), multiple-well sites, 

and wells having depth-dependent data (2005-2008), Eastern San Joaquin Ground-Water 

Subbasin, California.
Introduction

Arsenic occurs naturally in the 

earth’s crust and concentrations in water 

can be as high as 5,000 μg/L (Smedley 

and Kinniburgh, 2002). High concentrations in ground water may be present as 

a result of (1) geologic sources such as 

the weathering of sulfide minerals, (2) 

geochemical conditions in oxic (oxygen 

present) alkaline ground water, and in 

reducing (oxygen absent) ground water, 

(3) evaporation in closed basins in arid 

areas, or (4) in association with volcanic 

rocks or geothermal waters (Welch and 

Stollenwerk, 2003). Arsenic can be present in water as either arsenite (As III) 

or arsenate (As V). As(III) is more toxic 

than As(V)—although both forms are 

toxic, and the MCL for drinking water is 

for total arsenic. 

In January 2006, the U.S. Environmental Protection Agency MCL for 

arsenic in drinking water was reduced 

from 50 to 10 micrograms per liter 

(μg/L) in response to recent information 

concerning the risk of lung and bladder cancers (Morales and others, 2000). 

About 5 percent of water systems in 

the United States, serving more than 11 

million people, were expected to exceed 

the new MCL (Tienmann, 2001). Arsenic 

in excess of the MCL is of particular 

concern for ground-water supplies in 

parts of New England, the interior plains, 

and the western United States (Federal 

Register, 2001; Welch and others, 2000). 

Large spatial variability in arsenic concentrations within aquifers often makes 

it difficult to predict where high-arsenic 

water will be encountered (Smedley and 

Kinniburgh, 2002). Increased knowledge of the occurrence and distribution 

of arsenic in ground-water, especially 

its distribution with depth, may lead to 

management strategies and changes in 

well-construction practices designed 

to avoid the pumping of high-arsenic 

ground water. This may reduce the need 

for arsenic removal by expensive treatment, or the need to blend water from 

different sources to reduce arsenic concentrations in water served to consumers. 

Modification of existing wells to exclude 

high-arsenic ground-water may reduce 

the need to abandon wells that do not 

meet the current MCL.

The purpose of this paper is to 

present preliminary (2008) results from 

an ongoing study of geochemistry and 

recharge to wells in the Eastern San 

Joaquin Ground-Water Subbasin. The 

scope of the study included test-drilling, 

geophysical logging, water-quality data 

collection, well-bore flow logging, and 

depth-dependent water-quality sampling. 

The study approach coupled a basinwide areal assessment of arsenic concentrations with more detailed data collected 

from long-screened wells in areas with 

high-arsenic concentrations. The study 

evaluated the modification of a well 

to exclude water from depths having 

undesirable concentrations of arsenic as 

a management option to reduce arsenic 

concentrations in water from publicsupply wells. A two-dimensional, radial 

ground-water flow model was developed 

to evaluate the long-term effectiveness of 

the well modification. 

Hydrogeology

The study area is the Eastern San 

Joaquin Ground-Water Subbasin near 

Stockton, California, about 80 miles 

(mi) east of San Francisco (fig. 1). The 

ground-water subbasin is about 1,100 

mi2 (California Department of Water 

Resources, 2003), and is part of the 

larger San Joaquin Ground-Water Basin 

that forms the southern two-thirds of the 

Central Valley of California. The climate 

is characterized by hot, dry summers, 

and cool, moist winters. Average annual 

precipitation ranges from about 10 to 

18 inches. Precipitation is greater in the 

Sierra Nevada, to the east of the study 

area. Runoff from these mountains, 

primarily as snowmelt, sustains flows in 

the Mokelumne and Stanislaus Rivers 

that bound the study area to the north 

and south. The San Joaquin River, which 

drains the San Joaquin Valley from 

south to north, bounds the study area to 

the west, and the foothills of the Sierra 

Nevada bound the study area to the east 

(fig. 1).

The study area is underlain by 

several thousand feet of consolidated, 

partly-consolidated, and unconsolidated 

sedimentary deposits (California Department of Water Resources, 1967). The 

oldest deposits are marine and generally 

contain saline water, except where they 

crop out near the foothills of the Sierra 

Nevada. Regional ground-water flow in 

the San Joaquin Valley is through these 

marine deposits from recharge areas in 

the south to discharge areas near the San 

Joaquin delta. The marine deposits are 

separated from overlying sedimentary 

deposits by low-permeability volcanic 

deposits known as the Mehrten formation (Curtis, 1954). The volcanic 

deposits are about 1,000 feet (ft) below 

land surface in the Stockton area, and 

at shallower depths to the east toward 

the foothills of the Sierra Nevada. In 

the study area, the volcanic deposits are 

blanketed by a layer of alluvium eroded 

from the volcanic deposits (California 

Department of Water Resources, 1967). 

The overlying sedimentary deposits are 

divided into alluvial deposits eroded 

from the Sierra Nevada and its foothills, 

and the fluvial and delta deposits of the 

San Joaquin River. 

Under predevelopment conditions, 

the direction of ground-water flow in 

the alluvial deposits was from recharge 

areas in the east toward discharge areas 

near the San Joaquin delta. Within the 

study area, ground-water recharge to 

these deposits is about 900,000 acre-feet 

per year (acre-ft/yr) (CDM, Inc., 2001). 

Pumping for municipal and agricultural 

supply exceeds recharge by 150,000 

acre-ft/yr (CDM, Inc., 2001), and a 

large regional pumping depression has 

developed east of the city of Stockton. 

In 2000, the study area had a population of about 580,000 and population is 

expected to increase to more than 1.2 

million by 2040 (CDM, Inc., 2001).

Sources of Arsenic

In the study area, arsenic is weathered from minerals in volcanic deposits, 

in alluvium eroded from granitic rocks 

in the Sierra Nevada, and in alluvium 

eroded from metamorphic and volcanic rocks in the foothills of the Sierra 

Nevada. Sulfide minerals, associated 

Arsenic in Water from Wells

U.S. Department of the Interior 2

U.S. Geological Survey

October 2008
with metamorphic rocks and volcanic deposits in the foothills, are more 

abundant and contain greater amounts of 

arsenic than minerals in granitic rocks 

that compose the Sierra Nevada (Brown 

and Allan, 1955). As a consequence, 

smaller streams that drain the lower altitudes of the foothills may have eroded 

and deposited alluvium having greater 

abundance of arsenic than larger streams, 

such as the Mokelumne and Stanislaus 

Rivers, which drain the higher altitudes 

of the Sierra Nevada.

Iron-sulfide minerals, such as 

pyrite, commonly contain arsenic substituted within the crystal structure. Pyrite 

may originate as a primary mineral 

eroded from source rock or as a secondary mineral formed within aquifer deposits. Octahedral pyrite crystals (fig. 2), 

interpreted to be a primary mineral, 

were found in drilling samples collected 

from the volcanic deposits and alluvium 

eroded from those deposits. These crystals contained between 1 and 4 percent 

arsenic by weight. Some crystals show 

evidence of weathering and dissolution 

that may release arsenic to ground water. 

Twinned-pyritohedron crystals, interpreted to be a secondary mineral formed 

within aquifer deposits, also were found 

in drilling samples from the study area. 

Although incorporation of arsenic into 

secondary minerals could remove arsenic 

from ground water, arsenic was not 

detected within the crystal structure of 

secondary pyrite minerals (fig. 2).

 2N6E-11H4-8, 540 to 600 feet below LSD,

4 percent arsenic by weight

100 micrometers 100 micrometers

 2N6E-1A1-5, 540 to 600 feet below LSD,

0 percent arsenic by weight

Figure 2. Scanning electron photomicrographs of pyrite crystals from selected drilling 

samples, Eastern San Joaquin Ground-Water Subbasin, California.

Although the ultimate geologic 

source of arsenic is mineral weathering, 

arsenic sorbed to iron and manganese 

hydroxides on the surfaces of mineral 

grains may be more readily released to 

ground water than arsenic bound within 

the crystal structure of minerals. For 

example, under oxic conditions at alkaline pH’s, arsenic may be mobilized into 

ground water by exchange with arsenic 

sorbed to iron and manganese hydroxide 

coatings on mineral surfaces (Welch and 

others, 2000). Under reducing conditions, 

arsenic may be mobilized into ground 

water as these coatings dissolve (Welch 

and others, 2000).

Acid-extractable arsenic concentrations provide a measure of the arsenic 

sorbed on mineral grains. Acid-extractable concentrations in core material and 

drill cuttings collected as part of this 

study ranged from 0.05 to 1.6 mg / kg 

of alluvium. These concentrations are 

not unusual compared to the average 

continental abundance of arsenic (Hem, 

1985). Arsenic sorbed on the surface 

of mineral grains is a large reservoir of 

arsenic in the study area, with the highest concentrations in the fine-grained, 

organic-rich delta deposits. As much as 

90 percent of the acid-extractable arsenic 

was in the oxidized form, with a median 

of 64 percent as As(V). Most of the 

reduced arsenic, As(III), was associated 

with either organic or sulfur complexes. 

Concentrations in ground water are not 

limited by the availability of arsenic 

sorbed on mineral grains; instead specific 

geochemical conditions, especially redox 

and pH, within aquifers control arsenic 

concentrations in ground water.

Arsenic in Water from Wells

Occurrence and distribution of 

arsenic in public-supply and irrigation 

wells in the San Joaquin Valley of California was described by Belitz and others 

(2003). Although arsenic concentrations 

in most wells were generally less than 

5 μg/L, about 13 percent of wells in the 

San Joaquin Valley had concentrations 

in excess of 10 μg/L. Belitz and others 

(2003) identified ground water near the 

margin of the San Joaquin Delta as having high-arsenic concentrations.

Arsenic concentrations in water 

from wells the Eastern San Joaquin 

Ground-Water Subbasin ranged from 

less than the reporting limit (1 to 4 μg/L, 

depending on the method of analysis) to 

60 μg/L, with a median concentration of 

6 μg/L (fig. 1). These data are based on 

1,190 samples collected from more than 

250 wells between 1974 and 2004 by 

federal, state, and local agencies. Only 2 

samples were greater than the previous 

MCL for arsenic of 50 μg/L, while about 

26 percent of the samples were greater 

than the MCL of 10 μg/L. Arsenic concentrations in samples collected from 50 

wells as part of this study between May 

2004 and February 2007 were similar and 

ranged from 1 to 63 μg/L with a median 

concentration of 5.1 μg/L. About onethird of those samples were greater than 

the MCL of 10 μg/L. Water from wells 

having arsenic concentrations greater 

than 10 μg/L can no longer be used as a 

source of public supply without treatment 

or blending.

Arsenic concentrations in water 

from wells were not uniformly distributed 

areally or with depth in the study area 

(fig. 1). Arsenic concentrations were less 

than 10 μg/L in the eastern part of the 

study area near ground-water recharge 

areas along the foothills of the Sierra 

Nevada. Arsenic concentrations increased 

to the west, and high concentrations were 

distributed in a northwest trending band 

near the margin of the San Joaquin Delta 

(fig. 1). This is similar to the distribution 

OFR 2008-1272

U.S. Department of the Interior 3

U.S. Geological Survey

October 2008
of high-chloride water in the study area 

(Izbicki and others, 2006).

Arsenic concentrations in water 

from the surface discharge of wells 

generally increased with well depth. The 

probability that water from a well would 

have an arsenic concentration greater 

than or equal to the MCL of 10 μg/L 

was 21 percent for wells less than 330 ft 

deep, 39 percent for wells between 330 

and 500 ft deep, and 48 percent for wells 

greater than 500 ft deep (fig. 3). This 

relation with well depth varied spatially. 

For example, there was no correlation 

between well depth and arsenic concentrations in the eastern part of the study 

area where arsenic concentrations were 

generally low. In contrast, along the western side of the study area adjacent to the 

San Joaquin Delta, arsenic concentrations 

were commonly greater than 10 μg/L, 

regardless of well depth. 

Well-bore flow and depth-dependent 

water-quality data were collected from 

11 wells in the subbasin (fig. 1). Data 

from well 1N/7E-20N1 (fig. 4) illustrate 

the depth-dependence of arsenic concentrations in wells within the study area. 

Within well 20N1, about 55 percent of 

the water was yielded from the upper part 

of the screened interval between 158 and 

204 ft below land surface. Water from 

these shallower depths had an arsenic 

concentration about 5 μg/L. In contrast, 

water from deeper depths had arsenic 

concentrations in excess of 15 μg/L 

(fig. 4). The higher concentrations were 

masked by mixing within the well as 

water was pumped to the surface. Water 

from well 20N1 has a history of arsenic 

10

0

20

30

40

50

60

70

100 80 60 40 20 0 100 80 60 40 20 0

10

0

20

30

40

50

60

70

ARSENIC, IN MICROGRAMS PER LITER

Less than 330

330 to 500

Greater than 500

PERCENT EQUAL TO OR GREATER THAN 

7.5 to 7.9

Greater than 7.9 34

138

67

Depth to bottom of deepest well screen, in feet Sample pH, in standard units

Maximum

Contaminant

Level

139

53

43 Maximum

Contaminant

Level

Less than 7.5

Figure 3. Cumulative distribution of average arsenic concentrations in water from wells as 

a function of well depth and pH, Eastern San Joaquin Ground-Water Subbasin, California, 

1974 to 2004. Number in figure is numbers of wells within each group.

0 100

FLOW,

IN PERCENT

OF TOTAL

WELL

CONSTRUCTION 

0 100 0 10 0 20

100

200

300

400

0 100

RESISTIVITY,

IN OHM-METERS 

DEPTH, IN FEET BELOW LAND SURFACE

6 9

Access tube

pH, IN

STANDARD

UNITS

ARSENIC, IN

MICROGRAMS

PER LITER

NITRATE, IN

MILLIGRAMS

PER LITER

AS NITROGEN

CHLORIDE,

 IN MILLIGRAMS

PER LITER

EXPLANATION

Measured values Surface

 discharge

Screened interval

Calculated values Pump intake Direction of flow

Pumping water level

Pump rate equals 2,300 gallons per minute; unpumped water level is 69.3 feet below land surface

Figure 4. Well-bore flow and depth-dependent water-quality data from well 1N/7E-20N1, 

Eastern San Joaquin Ground-Water Subbasin, California, August 2004.

concentrations greater than the MCL of 

10 μg/L, although at the time of sample 

collection well 20N1 had an arsenic concentration of 8.9 μg/L, slightly below the 

MCL. In contrast to arsenic, chloride and 

nitrate concentrations were higher in the 

upper part of well 20N1 (fig. 4). Highchloride and high-nitrate concentrations 

are probably the result of agricultural 

activities that altered the quality of shallow ground water. 

pH, Redox, and Microbiological 

Controls

Arsenic concentrations in water 

from the surface discharge of wells 

increased with pH (fig. 3). The probability that water from a well would 

have an arsenic concentration greater 

than or equal to the MCL of 10 μg/L was 

7 percent if the pH was less than 7.5, 29 

percent if the pH was between 7.5 and 

7.9, and 69 percent if the pH was greater 

than 7.9. The pH dependence of arsenic 

is consistent with results of previous 

work in the San Joaquin Valley (Belitz 

and others, 2003). pH was not uniformly 

distributed throughout the study area, and 

was generally lower in the eastern part of 

the study area and higher in deep wells 

farther downgradient.

Arsenic in Water from Wells

U.S. Department of the Interior 4

U.S. Geological Survey

October 2008
ARSENIC, IN MICROGRAMS PER LITER

y = 0.17x + 7.2

R2 = 0.56

pH, IN STANDARD UNITS

0 2 4 6 8

7

7.5

8

8.5

ARSENIC V, IN MIGROGRAMS PER LITER

ARSENIC, IN MICROGRAMS PER LITER

1-to-1 Correlation line

All arsenic present

as Arsenic V

20

0

0 20 40 60 80

40

60

Arsenic V

predominates

Arsenic III

predominates

Reducing, dissolved oxygen less than

 or equal to 0.5 milligrams per liter

Oxic, dissolved oxygen more than

 0.5 milligrams per liter

Oxic, inferred from iron less than detection

 limit of 6 micrograms per liter 

Reducing, inferred from iron concentrations

 greater than 13 micrograms per liter 

EXPLANATION

Wells near

Stanislaus and

Mokelumne Rivers

Figure 5. Arsenic V as a function of arsenic (total dissolved), and pH as a function of 

arsenic (total dissolved) in water from wells, Eastern San Joaquin Groundwater Subbasin, 

California, 2006.

Arsenic concentrations in oxic water 

from wells were less than the MCL of 

10 μg/L, and concentrations in these samples increased with pH (fig. 5), consistent 

with exchange of arsenic sorbed to iron 

and manganese hydroxides on mineral 

grains (Smedley and Kinniburgh, 2002). 

Two wells located near the Stanislaus and 

Mokelumne Rivers differed from other 

sampled wells and may have a different 

hydrologic and geochemical history than 

the other samples with respect to arsenic. 

Oxic ground water does not persist within the flow system, and arsenic 

concentrations in reduced water from 

wells ranged from 3 to 63 μg/L, with a 

median concentration of 10 μg/L (fig. 5). 

Increases in arsenic concentrations under 

reducing conditions are consistent with 

reductive dissolution of iron and manganese hydroxide coatings on mineral 

grains (Smedley and Kinniburgh, 2002). 

Arsenic in reduced ground water within 

the study area was positively correlated 

Figure 6. Well-bore flow and depth-dependent water-quality data (including total arsenic, 

arsenic III, and arsenic V) concentrations from well 2N/6E-12J1 in the Eastern San Joaquin 

Ground-Water Subbasin, California, August 2006.

0 100

FLOW,

IN PERCENT

OF TOTAL

WELL

CONSTRUCTION 

0 10 0 10 0 10

100

200

300

400

500

DEPTH, IN FEET BELOW LAND SURFACE

0 100 6 9

RESISTIVITY,

IN OHM-METERS 

Access tube

PH, IN

STANDARD

UNITS

ARSENIC, IN

MICROGRAMS

PER LITER

Arsenic III

Arsenic V

TOTAL

ARSENIC, IN

MICROGRAMS

PER LITER

DISSOLVED

OXYGEN,

 IN MILLIGRAMS

EXPLANATION PER LITER

Measured values Screened interval

Pump intake Calculated values Direction of flow

Pumping water level

Pump rate equals 2,200 gallons per minute; unpumped water level is 66.3 feet below land surface

were less than would be expected given 

the abundance of these elements in the 

environment and suggests that iron and 

manganese may be subsequently precipitated and removed from solution.

The oxidized form of arsenic, As(V), 

predominated in water from the surface 

discharge of almost all sampled wells 

regardless of pH or redox status (fig. 5). 

Although As(III) concentrations in some 

wells were as high as 22 μg/L, only two 

wells near the San Joaquin Delta had 

As(III) concentrations greater than As(V) 

concentrations. Depth-dependent waterchemistry data from well 2N/6E-12J1 

shows that the fraction of As(III) 

increased with depth, as pH increased 

and dissolved oxygen concentrations 

decreased, until As(III) was the predominate form (fig. 6).

Microbially mediated reduction of 

As(V) to As(III) may occur within the 

ground-water-flow system as oxygen and 

other electron acceptors are consumed 

and increasingly anerobic conditions predominate. In laboratory experiments the 

reduction of As(V) to As(III) proceeds 

rapidly compared to sterile (heat-killed) 

controls (fig. 7). However, the predominance of As (V) on exchanges sites and 

in ground water suggests that reduction 

of As(V) to As(III) is slow under natural 

conditions within the study area.

OFR 2008-1272

U.S. Department of the Interior 5

U.S. Geological Survey

October 2008

with iron and manganese. The increase 

in iron and manganese concentrations 

with increasing arsenic concentration 
Management of Arsenic 

Concentrations

Two commonly used methods to 

reduce high-arsenic concentrations in 

water from public-supply wells are treatment at the surface discharge, or blending 

of high-arsenic water with water from 

another source having lower arsenic 

concentrations. Another potentially cost 

effective method is modification of the 

well to exclude water from depths having 

undesirable concentrations of arsenic (or 

other constituents). 

Well modification was used to 

lower arsenic concentrations from well 

1N/7E- 20N1. This public-supply well 

had a history of arsenic concentrations 

above the MCL of 10 μg/L. Well-bore 

flow and depth-dependent water-quality 

data show that the high-arsenic concentrations in the surface discharge of 

the well result from high-arsenic water 

entering the well from aquifer deposits 

below about 280 ft (fig. 4). Modification of well 20N1 to eliminate the three 

deepest well screens and exclude water 

from the deeper deposits was expected 

to decrease concentrations in the surface 

discharge of the well to about 5 μg/L—

similar to the arsenic concentration in 

water from the shallower deposits above 

280 ft. Well-bore flow data suggest this 

would be accompanied by a corresponding decrease in well yield of about 45 

percent.

In May 2006, well 20N1 was modified by filling the part of the well below 

121 rows

600 feet

corresponds to results shown in figures 9 and 10

Simulated 

lithology

Hydraulic

conductivity,

in feet per day

Simulated well screens

For the purposes of modeling, the two

uppermost well screens from 158 to 188 and

196 to 204 feet were combined into one screen

Unsaturated zone (Inactive)

Silt

Clay

Gravelly sand

Clay and sand

Sand

Clay

Gravelly sand

Clay

Clay and sand

Clay

Interval, in feet

below land surface

Top Bottom

0

68

140

155

190

270

295

310

320

370

385

-

1

1

75

3

40

1

75

1

3

1

68

140

155

160

270

295

310

320

370

385

400

Top Bottom

158

282

312

360

196

298

326

390

Inactive grid—21 rows

Columns, variable width (multiplier 1.187),

total model width is 200,000 feet

Figure 8. Model grid, lithology, and wellscreen intervals used to simulate flow to 

well 1N/7E-20N1, Eastern San Joaquin 

Ground-Water Subbasin, California.

280 ft with low-permeability bentonite 

grout, thus sealing the bottom three well 

screens. A cap of sand was placed on top 

of the grout to complete the seal. The 

gravel pack, which extends the length of 

well 20N1 from the surface seal to 400 ft 

below land surface, was not altered. 

After modification, well 20N1 yielded 

water having an arsenic concentration of 

7 μg/L. This concentration was below 

the MCL, but higher than the concentration of 5 μg/L in aquifer deposits above 

280 ft. It is likely that water from deeper 

depths having high arsenic concentrations moved upward through the aquifer 

toward the remaining well screens. A 

radial ground-water flow model with 

particle tracking was constructed to simulate the movement of water in response 

to pumping from well 20N1. The model 

was used to evaluate measured changes 

in arsenic concentrations resulting from 

changes in well construction and subsequent upward movement of high-arsenic 

water from deeper depths.

Model development

The computer program MODFLOW 

(Harbaugh and McDonald, 1996) was 

used to simulate the response to pumping 

from well 20N1. The two-dimensional, 

radial model consisted of one layer representing a cylinder of aquifer material 

having a radius of 200,000 ft and a thickness of 400 ft (fig. 8). The radial extent of 

the model was larger than the influence 

of simulated pumping from the well. 

Regional ground-water flow and regional 

pumping effects were not simulated.

Hydraulic properties representing 

aquifer materials were assigned from 

lithologic and geophysical logs. Aquifer 

materials were assumed to be flat-lying 

and areally extensive throughout the 

cylinder. The model was calibrated by 

adjusting, within reasonable ranges, 

hydraulic conductivity values associated 

with the lithology assigned to individual 

model rows until there was a reasonable match between the simulated and 

measured distribution of flow within well 

20N1, and between the simulated and 

measured drawdown.

The computer program MODPATH 

(Pollock, 1994) was used to simulate the 

movement of water particles within the 

model domain. Each particle represents 

a discrete fraction of the well yield and 

a unique quality of water. The quality of 

water yielded by well 20N1 was calculated as the flow-weighted average of the 

particle concentrations. 

Simulated well construction was 

changed to determine the effect of 

modifying the well on arsenic concentrations in the surface discharge of water 

from well 20N1. Simulated results were 

compared to measured changes in arsenic 

concentration in water from the surface 

discharge of the well after the three deepest screens were backfilled with lowpermeability bentonite grout.

Additional details concerning model 

construction are available in Table 1.

Model results

Pumping was simulated at the rate 

of 2,300 gal/min for 1,000 days, and 

the model simulated drawdown of 58 

ft closely approximated the measured 

drawdown of 61 ft. Simulated drawdown 

Arsenic in Water from Wells

TIME, IN DAYS

ARSENIC, IN MICROGRAMS PER LITER

As V

experimental

As V sterile control

As III experimental

As III sterile control

100

50

0

0 5 10 15 20 25

150

Figure 7. Arsenic III and arsenic V 

concentrations with time of incubation in a 

slurry of core material, Eastern San Joaquin 

Ground-Water Subbasin, California.

U.S. Department of the Interior 6

U.S. Geological Survey

October 2008
400

300

200

100

0

400

300

200

100

0

400

300

200

100

0

400

300

200

100

0

0 100 200 300

DISTANCE FROM WELL, IN FEET

400 500 600

DEPTH, IN FEET BELOW LAND SURFACE

Simulated drawdown day 1

Simulated drawdown day 10

Simulated drawdown day 100

Simulated drawdown day 1,000

DRAWDOWN, IN FEET

Particle flowpath

1 10 100

Unsaturated zone

Screened

interval

Unsaturated zone

Unsaturated zone

Unsaturated zone

from pumping by the unmodified well 

was distributed throughout the aquifer 

(fig. 9). The simulated movement of 

water (illustrated as particles) to the well 

was primarily through coarse-grained 

deposits with smaller contributions from 

the intervening finer-grained deposits. 

Simulations show that near the water 

DEPTH, IN METERS BELOW LAND SURFACE

Simulated drawdown day 1

Simulated drawdown day 10

Simulated drawdown day 100

Simulated drawdown day 1,000

Unsaturated zone

Screened

interval

Unsaturated zone

Unsaturated zone

DRAWDOWN, IN FEET

Particle flowpath

1 10 100

400

300

200

100

0

Bentonite

backfill

400

300

200

100

0

400

300

200

100

0

400

300

200

100

0

0 100 200 300

DISTANCE FROM WELL, IN FEET

400 500 600

Unsaturated zone

Figure 10. Simulated pressure response 

and particle movement during pumping after 

modification of well 1N/7E-20N1, Eastern 

San Joaquin Ground-Water Subbasin, 

California.

table, water moved almost vertically 

downward until it encountered a coarsegrained layer and then moved rapidly 

towards the well. Finer-grained deposits 

in the deeper parts of the aquifer within 

500 ft of the well were still contributing water (particles) after 1,000 days of 

simulated pumping.

Pumping from the modified well 

was simulated at a rate 1,600 gal/min for 

1,000 days. The lower pumping rate was 

required to maintain water levels above 

the well screens, and reflects the expected 

lower yield from the modified well. 

Simulated drawdown from the modified 

well was focused at the upper screened 

interval (fig. 10). Water from deeper 

depths no longer entered the well directly, 

but instead moved upward through the 

aquifer deposits before entering the well. 

During the 1,000 day simulation, ground 

water from the deeper deposits contributed increasingly to the yield of the well, 

reaching a maximum of about 20 percent, 

increasing arsenic concentrations during 

the simulation (fig. 11). However, the 

volume of high-arsenic water yielded 

from the deeper deposits was less than 

the 45 percent of the volume of water 

yielded from those deposits prior to 

modification of the well.

The model was used to calculate the 

change in arsenic concentration in the 

surface discharge of well 20N1 if different screened intervals were backfilled 

with grout (fig. 11). The small change 

in the arsenic concentration as a result 

of filling the deepest screen interval was 

expected because of the small yield from 

that depth. Larger changes in arsenic 

concentrations were simulated as a 

result of the filling of the second and 

finally the third deepest screen intervals. 

Simulated arsenic concentrations were 

lower initially, but increased with time 

as water from deeper parts of the aquifer 

moved upward in response to pumping. 

The simulated arsenic concentration in 

the surface discharge of well 20N1 after 

the three deepest screens were filled with 

grout ultimately increased to a concentration of 7.2 μg/L after 1,000 days of 

pumping (fig. 11).

Simulated sealing of the gravel 

pack produced results that were only 

slightly different from results shown in 

figure 11. Despite its high-permeability, 

the gravel-packed packed annulus is not 

large enough to allow the movement of 

large quantities of high-arsenic water to 

the upper screen when the modified well 

is pumped. This suggests that relatively 

simple well modification strategies that 

only require backfilling the well and not 

OFR 2008-1272

U.S. Department of the Interior 7

U.S. Geological Survey

October 2008

Figure 9. Simulated pressure response 

and particle movement during pumping 

prior to modification of well 1N/7E-20N1, 

Eastern San Joaquin Ground-Water 

Subbasin, California.
the destruction of the well, casing, and 

surrounding gravel pack can be used to 

manage arsenic concentrations in water 

from wells.

Model Limitations

The two-dimensional radial flow 

model developed to interpret well-boreflow and depth-dependent water-quality 

data from well 1N/7E-20N1 is a simplified representation of the flow system 

around the well. The flat-lying areally 

extensive aquifer materials are not 

intended to accurately represent regional 

changes in subsurface geology, including 

the areal extent of these materials and 

the hydraulic connection between those 

materials. Similarly, the flat water table 

does not represent regional ground-water 

flow or interactions between pumping 

wells. However, this simplified radialflow model does provide a simple tool 

to evaluate the effects of changing well 

design on the quality of water that is 

discharged from a well.

Acknowledgements

This study was funded by the 

Northeastern San Joaquin Groundwater 

Banking Authority and the California 

Department of Water Resources, in cooperation with the U.S. Geological Survey. 

Additional water-chemistry data was provided as part of the U.S. Geological Survey’s Ground-Water Ambient Monitoring 

Assessment (GAMA) study funded by 

the California State Water Quality Board. 

The authors thank the County of San 

Joaquin and the California Department 

of Water Resources for their assistance 

with sample collection and analysis. The 

authors also thank the city of Stockton 

Municipal Utilities Department and other 

local water agencies for their support and 

access to wells during this study.

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K.R., Jurgens, Bryant, and Johnson, 

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modification of well 1N/7E-20N1, Eastern 

San Joaquin Ground-Water Subbasin, 

California.

TIME, IN DAYS

ARSENIC, IN MICROGRAMS PER LITER 4

0 200 400 600 800 1,000

5

6

7

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1

2

3

4

Simulated well screens—

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 360 to 390 feet (original well construction) 

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ofr20061309

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U.S. Department of the Interior 8

U.S. Geological Survey

October 2008

Arsenic in Water from Wells

For additional information on this report contact:

John A. Izbicki

4165 Spruance Rd. Suite 200

San Diego, CA 92101

(619)225-6131 e-mail: jaizbick@usgs.gov