Open File Report 2006-1309

5

5

580

205

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 50

50 to 100

100 to 250

Greater than 250

Chloride concentra-

 tion in water from

 wells, in milligrams

 per liter

Maximum extent of

 chloride concentra-

 tions greater than

 1,000 milligrams

 per liter in surface

 water of the

 San Joaquin Delta,

 1931 (Modified from

 Piper and others,

 1939)

Eastern San Joaquin

 Ground-Water

 Subbasin

EXPLANATION

STUDY

AREA

Pacific Ocean

Sierra Nevada

San

Francisco

Central

Valley

C

A

L I F

O

R

N I A

U.S. Department of the Interior

U.S. Geological Survey

November 2006

Figure 1. Chloride concentrations in water from wells in the Eastern San Joaquin 

Ground-Water Subbasin, California, 1984–2004.

Figure 2. Sources of high-chloride water to wells, Eastern San Joaquin Ground-Water 

Subbasin, California.

Introduction

As a result of pumping and 

subsequent declines in water 

levels, chloride concentrations have increased in water 

from wells in the Eastern San 

Joaquin Ground-Water Subbasin, about 80 miles east of 

San Francisco (Montgomery 

Watson, Inc., 2000). Water 

from a number of public-supply, agricultural, and domestic 

wells in the western part of 

the subbasin adjacent to the 

San Joaquin Delta exceeds the 

U.S. Environmental Protection 

Agency Secondary Maximum 

Contaminant Level (SMCL) for 

chloride of 250 milligrams per 

liter (mg/L) (fig. 1) (link to animation showing chloride concentrations in water from wells, 

1984 to 2004). Some of these 

wells have been removed from 

service. High-chloride water 

from delta surface water, delta 

sediments, saline aquifers that 

underlie freshwater aquifers, 

and irrigation return are possible 

sources of high-chloride water 

to wells (fig. 2). It is possible 

that different sources contribute 

high-chloride water to wells in 

different parts of the subbasin or 

even to different depths within 

the same well.

Sources of High-Chloride Water to Wells, Eastern San 

Joaquin Ground-Water Subbasin, California

By John A. Izbicki, Loren F. Metzger, Kelly R. McPherson, Rhett R. Everett, and George L. Bennett V

 1

EXPLANATION

Saline water in delta deposits

Unsaturated deposits

Freshwater aquifers

Bedrock Underlying saline aquifers

San Joaquin

River Irrigation return

Surface-water

infiltration

Contibutions from

 underlying deposits 

Dissolution of salts

 near delta margin 

Open File Report 2006-1309

Prepared in cooperation with Northeastern 

San Joaquin Groundwater Banking Authority

and California Department of Water Resources
Hydrogeology

The study area is the Eastern San 

Joaquin Ground-Water Subbasin near 

Stockton, California. The groundwater subbasin is about 1,100 square 

miles (California Department of Water 

Resources, 2006) and is part of the larger 

San Joaquin Ground-Water Basin that 

forms the southern half of the Central 

Valley of California. The climate of the 

area is characterized by hot, dry summers and cool, moist winters. Average 

annual precipitation ranges from about 10 

to 18 inches (Soil Conservation Service, 

1992). Precipitation is greater in the 

Sierra Nevada to the east of the study 

area. Runoff from those mountains, primarily as snowmelt, sustains flows in rivers and streams that cross the study area. 

The largest of these, the Mokelumne and 

Stanislaus Rivers, bound the study area 

to the north and south, respectively. The 

San Joaquin River, which drains the San 

Joaquin Valley to the south, 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). Volcanic deposits about 1,000 feet (ft) below 

land surface in the Stockton area, and 

at shallower depths to the east, separate overlying deposits from underlying 

marine deposits. Although they contain 

freshwater near the mountain front, the 

marine deposits contain saline water in 

most parts of the study area. The marine 

deposits have been explored for oil and 

gas and for the potential storage of waste. 

The overlying deposits can be divided 

into alluvial-fan deposits eroded from the 

Sierra Nevada, and delta deposits along 

the San Joaquin River. The alluvial-fan 

deposits are pumped extensively for water 

supply.

Under predevelopment conditions 

prior to the onset of ground-water pumping, ground-water movement in the alluvial-fan deposits was from the front of the 

Sierra Nevada to ground-water discharge 

areas near the San Joaquin Delta. Groundwater discharge to springs and seeps 

in this area was fresh and low in dissolved 

solids (Mendenhall, 1908). Surface water 

also infiltrated from the upstream reaches of 

rivers and streams into underlying alluvial 

deposits and ground water discharged along 

the downstream reaches of these streams 

(Piper and others, 1939). Regional groundwater movement in the San Joaquin Valley 

under predevelopment conditions was from 

south to north along the axis of the valley, 

with regional ground-water discharge to the 

delta. In a large part of the study area, ground 

water in deep wells completed below the volcanic deposits flowed to land surface under 

artesian conditions. Water from most of these 

deep artesian wells was saline (Mendenhall, 

1908) and not used for agricultural or public 

supply. Saline water extracted from deep 

wells, especially those used for natural gas 

production, was “allowed to waste” (Mendenhall, 1908), or in the Stockton area was used 

for recreational swimming pools because of 

its warm temperature (fig. 3). 

Figure 3. Recreational pools developed from 

saline ground water discharge in the San 

Joaquin Ground-Water Subbasin, Stockton, 

California, circa 1910. (Photograph courtesy of 

the Stockton Record.) 

In 2000, the study area had a population of about 580,000 (CDM, Inc., 2001), 

and population is expected to increase to 

more than 1.2 million by 2040 (CDM Inc., 

2001). Ground-water recharge is about 

900,000 acre-feet per year (acre-ft/yr), and 

pumping exceeds recharge by 150,000 acreft/yr. Water levels in parts of the subbasin 

declined to below sea level in the early 1950’s 

(California Department of Water Resources, 

1967). The pumping depression expanded 

and shifted eastward in recent years (link to 

animation showing changes in water-level 

contours, 1974 to 1999), and water levels 

in parts of the basin were declining at rates 

as high as 2 feet per year (Northeastern San 

Joaquin County Groundwater Banking Authority, 2004). Within the 

pumping depression, ground water 

flowed from recharge areas near the 

mountain front, from major streams 

and rivers, and from the San Joaquin 

Delta toward pumping wells. 

Purpose and Scope

The purpose of this report is to 

illustrate the types of data collected, 

and to present preliminary (2006) 

results from an ongoing study of 

the source of high-chloride water 

to wells in the Eastern San Joaquin 

Ground-Water Subbasin. The scope 

of the study includes test-drilling, 

geophysical logging, and identification of the source of high-chloride 

water to wells using geochemical 

techniques. The study couples a 

basin-wide areal assessment of 

water quality with more detailed 

geologic, geophysical, and geochemical data collection along geologic sections in the area affected by 

declining water levels and increasing chloride concentrations (fig. 4). 

Although beyond the scope of this 

preliminary report, extrapolation 

of data along the cross-sections is 

intended to extend detailed data collected from multiple-well monitoring sites and from large-capacity 

wells to other wells along the geologic sections. This approach will 

aid in the development and a more 

complete understanding of how the 

spatial and vertical distribution of 

subsurface geology, hydrology, and 

geochemistry combine to influence 

the movement of high-chloride 

water to wells.

Test Drilling and Well 

Installation

Test drilling and well installation was done to obtain samples 

of geologic materials, lithologic 

and geophysical logs, and to install 

wells for use as measuring points 

for water-level and water-quality 

data collection. Between May and 

October 2005, three multiple-well 

sites—each containing three to 

November 2006

U.S. Geological Survey

U.S. Department of the Interior

Sources of High-Chloride Water to Wells

 2
five 2-inch diameter monitoring wells 

with PVC casings installed at different 

depths, were completed. Data from these 

sites were supplemented with data from 

multiple-well sites installed previously at 

two locations by the California Department of Water Resources (2003), and at an 

additional location by the City of Stockton 

(fig. 4).

Geophysical logs and well-construction data for multiple-well site 2N/5E1A1–5, installed near the eastern edge of 

the San Joaquin Delta, are shown in figure 5. This site was selected because two 

wells less than one-half mile east of this 

site were removed from service as a result 

of high-chloride concentrations. Water 

levels at this multiple-well site ranged 

from about 13 to 27 ft below land surface 

in May 2005, and depth to water increased 

with well depth. The site is located in 

what would have been a ground-water 

discharge area under predevelopment conditions, and the increase in depth to water 

with well depth is probably the result of 

regional ground-water pumping. In May 

2005, chloride concentrations at this site 

ranged from 550 to 1,800 milligrams per 

liter (mg/L). At that time, the shallowest 

and deepest wells had chloride concentrations of 1,800 and 1,700 mg/L, 

Figure 4. Location of selected wells and geologic sections, Eastern 

San Joaquin Ground-Water Subbasin, California.

5

5

580

205

Lodi

Manteca

Stockton

0 5 10 15 Kilometers

0 5 10 15 Miles

San Joaquin

Delta

Mokelumne River

Stanislaus River

San Joaquin River

Eastern San Joaquin

 Ground-water

 Subbasin

Multiple well

 sites—

Well with

 velocity

 log data

Other

 sampled

 wells

USGS

City of

Stockton

Department

of Water

Resources

Geologic

section lines—

Ca

C

EXPLANATION

Ca

Ba

Da

D Aa

C

B

A

20E1-3

1A1-5

11H4-8

24P1-3

36C3-5

4J3-5

20N1

Figure 5. Selected geophysical logs and well-construction data for multiple-well 

site, 2N/5E-1A1–5, Eastern San Joaquin Ground-Water Subbasin near Stockton, 

California, May 2005.

200

400

600

800

1,000

0

Caliper,

in inches

Gamma, in counts

per second

Resistivity,

in ohm-meters

16 inch 

64 inch

Depth, in feet below land surface

4 12 20 0 100 200 0 10 20

1A11A21A3

Well number1A4

1A5

1,700

1,800

625

960

550

Number is chloride concentration

in milligrams per liter

respectively (fig. 5). Data from the wells 

at this site and from monitoring wells at 

other multiple-well sites will be used to 

evaluate the chemical and isotopic composition of potential sources of high-chloride 

water to these wells.

The two other multiple-well sites 

1N/6E-4J3–5 and 2N/6E-11H4–8 (fig. 4) 

were drilled to depths of 600 and 643 ft 

below land surface, respectively. In January 2006, chloride concentrations in water 

from sites -4J3–5 near the San Joaquin 

Delta ranged from 120 to 510 mg/L, with 

the highest concentration in well -4J4 that 

was completed between 360 and 340 ft 

below land surface. In May 2005, chloride concentrations in water from sites 

-11H4–8, near ground-water recharge 

ponds east of the delta, were between 9.9 

and 3.4 mg/L.

U.S. Department of the Interior

U.S. Geological Survey

November 2006

OFR 2006-1309

 3
Borehole Geophysical 

Data

In addition to geophysical logs 

collected during test drilling, two types of 

borehole geophysical data were collected 

as part of this study. Electromagnetic 

(EM) logs were collected from selected 

multiple-well sites to evaluate changing 

water quality at depth. Fluid-velocity logs 

were collected under pumping conditions from selected public supply wells to 

determine the depth at which water enters 

those wells. Velocity logs were coupled 

with depth-dependent water-quality data, 

also collected under pumping conditions, 

to determine the quality of water entering 

the well at different depths.

Electromagnetic logs

Only a limited number of wells 

screened over selected intervals can 

be installed at multiple-well monitoring sites. As a consequence, changes in 

water quality are not measured directly 

through much of the aquifer thickness. To address this issue, the deepest 

well at multiple-well sites was used as 

access tubes for repeated measurement 

of electromagnetic resistivity through 

the entire aquifer thickness penetrated 

by the well. EM logs collected through 

the PVC casings of monitoring wells are 

sensitive to the lithology of the deposits 

and to the resistivity of the pore fluids 

within the deposits (McNeill and others, 

1990). Because the lithology remains 

constant with time, repeated EM logs 

differ only if the fluid resistivity changes 

as a result of the movement of water of 

differing quality at depth (Williams and 

others, 1993). The radius of the material 

measured by the logging tool is between 

10 and 50 inches, and as a result the tool 

is relatively insensitive to borehole fill 

material adjacent to the well (McNeill 

and others, 1990). These properties make 

EM resistivity a suitable tool for identifying changes in water quality, particularily changes in salinity, at locations from 

which ground-water samples cannot be 

collected directly.

EM resistivity values at corresponding depths from logs collected within well 

2N/6E-20E1 in June 2004 and 

Figure 6. Comparison of electromagnetic 

resistivity values collected in well 2N/6E-20E1, 

Eastern San Joaquin Ground Water Subbasin 

near Stockton, California.

January 2006 are shown in figure 6. In the 

time between collection of the two logs, 

EM resistivity values decreased in a narrow 

interval between 400 and 402 ft below land 

surface (fig. 6). The January 2006 values, 

between 400 and 402 ft, were among the 

lowest collected from the well. Because the 

lithology has not changed, decreased EM 

resistivity at this depth may be the result of 

decreased fluid resistivity (increased fluid 

conductivity) resulting from increased salinity between the two logging dates. Horizontal movement of poor-quality water through 

thin, permeable zones that are either areally 

extensive, or well-connected hydraulically, 

commonly occurs in coastal California 

aquifers (Nishikawa, 1997). Given this scenario, the three monitoring wells at this site 

(screened from 472 to 507, 289 to 319, and 

189 to 209 ft below land surface, respectively) would not have detected changes in 

water quality that caused changes in EM 

resistivity observed near 400 ft.

Decreases in EM resistivity consistent 

with increasing chloride concentrations also 

were observed between 40 and 45 ft below 

land surface in EM logs collected from well 

1N/6E-36C3 between June 2004 and January 

2006. Previous work (California Department of Water Resources, 1967) indicated 

the presence of poor-quality water near the 

water-table in this part of the study area and 

suggested that this shallow ground water 

may have been the source of high-chloride 

water in some production wells. 

Additional EM 

logging at these sites 

would be required 

to determine if EM 

resistivity values 

will continue to 

decrease through 

time. Additional data 

collection, possibly 

including the installation of new wells, 

may be required to 

determine if changes 

in EM resistivity are 

the result of changes 

U.S. Department of the Interior

U.S. Geological Survey

 4 November 2006

1

1

10

10

Electromagnetic resistivity, in ohm-meters, June 2004

EXPLANATION

Electromagnetic resistivity, in ohm-meters, January 2006

400-402 feet

All other data

1

1

10

100

10 100

in water quality or the result of some 

other cause.

Fluid-velocity logs and depthdependent water-quality 

sample collection

Fluid-velocity logs from 

unpumped and pumped wells were 

collected using an EM flowmeter. 

The EM flowmeter measures uphole 

or downhole velocities according 

to Faraday’s Law, where the voltage generated by the movement of 

charged ions in water flowing through 

an induced magnetic field is proportional to the velocity of water flowing 

through the field. The tool has a range 

from 0.3 to 260 feet per minute, and is 

suitable for both the low velocities in 

unpumped wells and the high velocities in pumped wells (Newhouse and 

others, 2005). Fluid resistivity and 

fluid temperature data collected during 

logging were used to constrain interpretations of fluid-velocity logs. 

Fluid-velocity logs from pumped 

wells were coupled with water-quality samples collected under pumping 

conditions from selected depths within 

the well. Sample depths were selected 

on the basis of measured velocity logs, 

lithologic logs, geophysical logs, and 

well-construction data. The samples 

were collected using a commercially 

available, small-diameter gas-displacement pump (Izbicki, 2004). Water 

samples collected using this method 

are mixtures of water that entered the 

well from different depths. However, 

when coupled with velocity log data, 

Sources of High-Chloride Water to Wells
depth-dependent water-quality data can 

be used to estimate the quality of water 

entering a well from selected depths in an 

aquifer (Izbicki, 2004).

Fluid-velocity logs from well 

1N/7E-20N1 show that slightly more than 

one-half of the water entered well -20N1 

through the two upper screens located 158 

to 204 ft below land surface (fig. 7). Most 

of the remaining water entered the well 

through screens at 282 to 298 and 312 to 

326 ft below land surface. Only a small 

amount of water entered the well through 

the deepest screen 360 to 390 ft below 

land surface (fig. 7). In well -20N1, the 

higher yielding upper zones correspond to 

electrically resistive sand and gravel units 

indicated on the electric log (fig.7). Where 

present in other wells, this high-resistivity zone also contributes large amounts of 

water to wells. The small amount of yield 

from the deepest screen was unexpected 

on the basis of lithologic and geophysical 

logs, and may reflect increased consolidation and decreased hydraulic conductivity of alluvial deposits with depth.

Depth-dependent water-quality 

samples collected within well -20N1 

under pumping conditions reflect the 

vertical distribution of water-quality 

within the aquifer (fig. 7). Chloride 

and nitrate concentrations are higher 

in water entering from the upper well 

screens than the deeper well screens. In 

contrast, pH and arsenic concentrations 

were higher in water entering from 

the deeper parts of the well. Arsenic 

concentrations in the deeper parts of 

well -20N1 were as high as 15 micrograms per liter (mg/L). Mixing of water 

having lower arsenic concentrations 

from shallower depths within the well 

caused water discharge at the surface 

to approach the Maximum Contaminant Level (MCL) for arsenic of 10 

mg/L (U.S. Environmental Protection 

Agency, 2006). Changes in well 

drilling and construction practices 

could exclude zones having high 

concentrations of constituents such as 

chloride, nitrate, or arsenic from newly 

installed wells, and modifications in well 

design could exclude zones contributing 

poor-quality water to existing wells—

thereby improving the quality of water 

from those wells.

By January 2006, fluid velocity logs 

coupled with depth-dependent water-quality data had been collected from eight 

wells that are distributed along the sections shown in figure 4. Data from these 

wells will be used with geochemical data 

collected from the surface discharge of 

wells throughout the study area to determine the sources of high-chloride water to 

wells.

Sources of High-Chloride 

Water to Wells

Prior to the construction of reservoirs 

on rivers tributary to the San Joaquin 

Delta, water having chloride concentrations as high as 1,000 mg/L intruded the 

delta during low-flow periods (Piper and 

others, 1939) (fig. 1). Under present-day 

(2006) conditions, surface flows are managed to protect freshwater resources in the 

delta and to prevent the inland movement of seawater. However, high-chloride 

water may originate from water trapped 

in delta sediments during their deposition—constituents dissolved within this 

water may retain a chemical composition 

consistent with a seawater origin. Highchloride water also may originate from 

soluble salts emplaced in sediments from 

ground-water discharge along the delta 

margin—constituents dissolved within this 

water would have a chemical composition 

different from seawater. It is likely that 

water from deeper aquifers that underlie 

freshwater aquifers pumped for supply 

also has markedly different chemical 

composition and may contribute highchloride water to wells in different parts of 

the subbasin. In addition, irrigation return 

may increase chloride concentrations near 

the water table. To further complicate the 

issue, multiple sources of high-chloride 

water may occur at different depths within 

the same well. Water from wells was sampled and analyzed for major-ions, selected 

minor ions, and its isotopic (oxygen-18 

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

Figure 7. Fluid velocity and depth-dependent water-quality data from well 1N/7E20N1, Eastern San Joaquin Ground-Water Subbasin, California, August 2004.

U.S. Department of the Interior

U.S. Geological Survey

November 2006

OFR 2006-1309

 5
and deuterium) composition, to determine 

the composition of fresh and high-chloride 

waters in the study area and the sources of 

high-chloride water to wells.

Major-Ion Composition of Water 

from Wells

The major-ion composition of 100 

water samples from 76 public-supply, 

irrigation, domestic, and observation wells 

collected as part of this study between 

May 2004 and January 2006, and 245 

historical samples from 42 wells were 

evaluated using a trilinear diagram (fig. 8). 

A trilinear diagram shows the proportions 

of the major cations (calcium, magnesium, 

and sodium plus potassium) and the major 

anions (carbonate plus bicarbonate, sulfate, and chloride) on a charge-equivalent 

basis (Hem, 1985). Cations are plotted on 

the lower left triangle, anions on the lower 

right triangle, and the central diamond 

integrates the data. 

On the basis of their distribution 

within the trilinear diagram, data were 

separated into three groups having 

different chemical compositions. Group 

1 represents the majority of sampled 

wells. Group 2 consists of depthdependent samples from deeper depths 

within sampled public-supply wells, 

and samples from deeper observation wells at multiple-well sites. The 

composition of water from deeper 

aquifers represented by these samples 

is not apparent in historical data collected from the surface discharge of 

wells; because ground water from 

deeper depths mixes within the wells 

with ground water from shallow depths 

during pumping, thereby masking 

the composition of the deeper ground 

water. As a result of mixing within the 

well during pumping, samples from the 

surface discharge public-supply wells 

plot within Group 1 even though deeper 

samples from the same well plot within 

Group 2. All samples within Groups 

1 and 2 had chloride concentrations 

of less than 100 mg/L. In contrast, all 

but two samples within Group 3 were 

from wells that had chloride concentrations greater than 100 mg/L. This group 

included several public-supply wells 

that are no longer in use due to chloride 

concentrations that were greater than the 

Secondary Maximum Contaminant Level 

(SMCL) of 250 mg/L (U.S. Environmental Protection Agency, 2006). The majorion composition of water from wells did 

not trend consistently toward the composition of seawater as chloride concentrations 

increased. 

Minor-Ion Composition of Water 

from Wells

Certain minor ions in water, such as 

bromide, iodide, barium, and boron are 

present naturally in high-chloride water 

from different sources, and have been 

used to determine the origin of high-chloride water to wells (Piper and Garrett, 

1953; Izbicki and others, 2005). Analysis of this combination of minor ions is 

especially effective because their differing abundances, chemical properties, and 

biological reactivity can produce a wide 

range of compositions, relative to chloride concentrations; these compositions 

reflect different geology, source-water 

composition, and aquifer chemistry. Of 

the four minor ions analyzed in this study, 

iodide commonly has the largest range in 

environmental compositions, relative to 

chloride and is commonly very useful in 

determining the source of high-chloride 

water to wells.

Iodide is depleted in seawater 

through uptake by marine organisms 

(Izbicki and others, 2005). As these 

organisms die, are buried, and decay, 

water within marine deposits may become 

enriched in iodide. In the plot of chlorideto-iodide ratio as a function of chloride 

(fig. 9), data are bimodally distributed 

and reflect contributions of high-chloride 

water from at least two sources. The chloride-to-iodide ratio from some wells follows a seawater mixing line with increasing chloride concentrations, and reflects 

high-chloride seawater minimally altered 

by contact with aquifer material.

Water from most observation wells and 

from depth-dependent samples collected 

within the deeper parts of public-supply 

wells plotted to the right of the seawater 

mixing line. The iodide-enriched composition of water from these wells is similar 

to that of water from marine rocks and 

oil-field brine sampled elsewhere in 

80

60

40

20

20

40

60

80

20

40

60

80 80

60

40

20

20

40

60

80

20

40

60

80

California Department of Water

 Resources data (1969-2003)

Public-supply, irrigation, or domestic

 well surface discharge sample 

Other sampled wells

Multiple well site

Depth-dependent sample

Surface discharge sample from depth-dependent sampled well

U.S. Geological Survey data (2001-05)

Seawater

Magnesium

Sulfate

Carbonate + Bicarbonate

Sulfate + Chloride

Calcium Chloride

Calcium + Magnesium

PERCENTAGE OF TOTAL MILLIEQUIVALENTS PER LITER

PERCENTAGE OF TOTAL MILLIEQUIVALENTS PER LITER

EXPLANATION

Group 1

Group 2

Group 3

11H1

11H2

11H3

11H4

1A5

1A4 1A3

1A2

1A1

Sodium + Potassium

Figure 8. Major-ion chemistry of water from selected wells in the Eastern San 

Joaquin Ground-Water Subbasin, California, 2004–2005.

U.S. Department of the Interior

U.S. Geological Survey

OFR 2006-1309

November 2006 6

Sources of High-Chloride Water to Wells
0.01 0.1 1 10 100 1,000

EXPLANATION

Seawater

1A5

Reactions with marine rock

100

1,000

10,000

100,000

1,000,000

10,000,000 Chloride-to-iodide molar ratio

Multiple well sites

Depth-dependent samples

Other sampled

 wells Mixing line

Chloride, in millimoles per liter

Chloride, in milligrams per liter

10 100 1,000 10,000

California (Piper and Garrett, 1953; Izbicki 

and others, 2005). Several wells having 

high-chloride water, including the shallow 

observation well -1A5 at the Oak Grove 

Park multiple-well site, have chloride-toiodide ratios intermediate between compositions expected from seawater mixing and 

from deep brines. Water from these wells 

may be complex mixtures of high-chloride 

water from multiple sources, or the water 

may have reacted with aquifer materials to 

remove iodide from the solution.

Oxygen-18 and Deuterium 

Composition of Water from Wells

Oxygen-18 and deuterium are naturally occurring stable isotopes of oxygen 

and hydrogen, respectively. Oxygen-18 

(d18O) and deuterium (dD) abundances are 

expressed as ratios, in delta notation as 

per mil (parts per thousand) differences, 

relative to the standard known as Vienna 

Standard Mean Ocean Water (VSMOW). 

By convention, the value of VSMOW is 0 

per mil. Negative per mil values have more 

of the lighter isotope than VSMOW (Craig, 

1961), and highly negative per mil values 

have more of the lighter isotope than less 

negative values. 

Most of the world’s precipitation originates from the evaporation of seawater. As 

a result, the d18O and dD composition of 

precipitation throughout the world is 

correlated linearly and distributed along 

a line known as the global meteoric 

water line (Craig, 1961). In many areas, 

water samples plot along a line slightly 

below the global meteoric water line 

that is known as the local meteoric 

water line. The d18O and dD composition of a water sample, relative to the 

global meteoric water line and relative 

to the composition of water from other 

areas, provides a record of the source 

and evaporative history of the water, and 

can be used as a tracer of the movement 

of the water. Differences in the d18O 

and dD composition of water from the 

global meteoric water line may result 

from differences in the temperature 

of condensation of precipitation that 

recharged the ground water. These differences may result from condensation 

at different altitudes, from seasonal or 

short-term climatic changes, or from 

long-term climatic changes such as 

those that occurred at the end of the 

Pleistocene Epoch. Partial evaporation 

of a water sample shifts the d18O and dD 

composition to the right of the global 

meteoric water line along an evaporative 

trend line (International Atomic Energy 

Agency, 1981). 

The d18O and dD composition 

of water from wells in the study area 

ranged from –6.3 to –11.2 per mil 

and –48 to –81 per mil with a median 

composition of –8.4 and –60 per mil, 

respectively (fig. 10). Most samples plot 

parallel to, but below, the global meteoric water line.

The more negative values are from 

shallow wells, typically about 100 ft 

deep, along the Mokelumne and Stanislaus Rivers (fig. 10). These rivers drain 

the higher altitudes of the Sierra Nevada 

to the east of the study area, and water 

from these wells probably originated 

as precipitation at cooler temperatures 

associated with higher altitudes instead 

of precipitation at warmer temperatures 

associated with lower altitudes. There 

was no consistent trend toward increasingly negative values from deeper wells 

at multiple-well sites installed as part of 

this study. However, dD values between 

–70 and –68 per mil were obtained 

from shallower wells at a multiple-well 

site 2N/6E-11H4–8 near ground-water 

recharge ponds. These data are consistent 

with movement of recharge water from 

the ponds (that originated from reservoirs 

in the Sierra Nevada) to depths as great 

as 300 ft. 

The less negative samples plot to 

the right of the local meteoric water line 

along an evaporative trend line (fig. 10). 

Although most high-chloride water plots 

to the right of the meteoric water line, 

chloride concentrations do not consistently increase with the evaporative shift 

in d18O and dD isotopic composition. 

These data suggest that the high-chloride 

concentrations are the result of processes 

other than evaporative concentration of 

ground water, and are consistent with 

high-chloride water mobilized from delta 

sediments or deeper deposits. 

Summary

Water levels are declining and 

chloride concentrations are increasing in water from wells in the Eastern 

San Joaquin Ground-Water Subbasin 

near Stockton, California, as a result of 

pumping in excess of recharge. A study 

approach that utilizes a combination of 

data collection activities including (1) 

drilling and monitoring well installation, 

(2) borehole geophysical data collection 

from monitoring wells and large-capacity pumping wells, and (3) geochemical 

data collection was developed to evaluate 

the areal and vertical distribution of 

chloride within freshwater aquifers and 

Figure 9. Chloride-to-bromide and chlorideto-iodide ratios as a function of chloride 

concentration in water from selected wells 

in the Eastern San Joaquin Ground-Water 

Subbasin, California, 2004–2005. 

-90

-80

-70

-60

-50

-40

-12 -11 -10 -9 -8 -7 -6

delta oxygen-18, in per mil

delta deuterium, in per mil

Shallow wells

2N/6E-11H6–8 (Less than

300 ft deep)

Deeper wells

2N/6E-11H4–5

(Greater than

 300 ft deep)

Evaporative

trend line

Global meteoric water line

(Craig, 1961)

Shallow wells (less than 150 ft deep) near

the Mokelumne and Stanislaus Rivers

EXPLANATION

Chloride concentration, in milligrams per liter

Less than 100 100 to 250 Greater than 250

Figure 10. Oxygen-18 and delta deuterium 

composition of water from selected wells 

in the Eastern San Joaquin Ground-Water 

Subbasin, California, 2004–2005.

U.S. Department of the Interior

U.S. Geological Survey

November 2006

OFR 2006-1309

 7
to determine the sources of high-chloride 

water to wells. The study couples a basinwide areal assessment of water quality 

with detailed geologic, geophysical, and 

geochemical data collected along geologic 

sections in the area affected by declining water levels and increasing chloride 

concentrations.

Preliminary results show that water 

from multiple-well site 2N/5E-1A1–5 near 

the San Joaquin River Delta had chloride 

concentrations as high as 1,800 mg/L. 

High chloride concentrations were present 

at this site to almost 1,000 ft below land 

surface. EM logs collected from well 

2N/6E-20E1 north of Stockton showed 

decreased EM resistivity. EM logs collected in well 1N/6E-36C3 south of Stockton, showed decreases in EM resistivity 

at shallower depths between 40 and 45 ft 

below land surface. High-chloride water 

from shallow depths has been observed in 

production wells in this part of the study 

area. Additional EM logging at these sites 

would be required to determine if EM 

resistivity values continue to decrease 

through time and if decreasing resistivity 

is the result if increasing salinity.

Water-quality in the study area 

changes with depth, and the major-ion 

composition of water from deeper aquifers 

is obscured by mixing within wells during 

pumping. As a consequence, the composition of water from deeper deposits 

penetrated by wells is not apparent in 

historical data collected primarily from 

the surface discharge of wells. Changes 

in the iodide composition of water from 

wells with elevated chloride concentrations are consistent with a marine origin 

of the chloride dissolved in water from 

wells. Entrainment of seawater in delta 

deposits may have occurred during 

deposition of delta sediments. Subsequent 

mobilization of this entrained water may 

have occurred as a result of ground-water 

pumping. High-chloride water in deeper 

parts of the aquifer is enriched in iodide, 

relative to seawater compositions and also 

contributes to increasing chloride concentrations in water from some wells. Such 

enrichment is common in deeper ground 

water from oil- and gas-producing regions 

in California (Piper and Garrett, 1953; 

Izbicki and others, 2005). Shifts in the 

d18O and dD composition of water from 

some shallower wells are consistent 

with partial evaporation of water and 

irrigation return water. However, increases 

in chloride concentrations from evaporation of irrigation water are small compared to chloride inputs from the delta and 

underlying deposits.

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. The authors thank 

the County of San Joaquin, the California 

Department of Water Resources, and the 

California State Water Resources Control 

Board Ground-Water Ambient Monitoring and Assessment (GAMA) Study for 

their assistance with sample collection and 

analyses. The authors also thank the local 

water agencies for the support, and access to 

wells during this study—especially Brandon 

Nakagawa of the San Joaquin County Public 

Works Department, Anthony Tovar of the 

City of Stockton Municipal Utilities Department, and Eric Mar of the California Water 

Service Company.

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Available online at

http://pubs.water.usgs.gov/ofr2006-1309/

 8

Sources of High-Chloride Water to Wells