U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2017–1162

January 2018

U.S. Geological Survey and the California State Water Resources Control Board

Groundwater Quality in the Shallow Aquifers of the Madera–

Chowchilla and Kings Subbasins, San Joaquin Valley, 

California

Groundwater provides more than 40 percent of California’s drinking water. To protect this vital resource, the 

State of California created the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA 

Program’s Priority Basin Project assesses the quality of groundwater resources used for drinking-water supply and 

increases public access to groundwater-quality information. Many households and small communities in the Madera–

Chowchilla and Kings subbasins of the San Joaquin Valley rely on private domestic wells for their drinking-water supplies.

The Madera-Chowchilla and Kings Subbasins

The Madera–Chowchilla and Kings shallow aquifer study unit consists of groundwater 

resources in the Madera, Chowchilla, and Kings groundwater subbasins of the San Joaquin 

Valley that are used for private domestic drinking water supply. Over 150,000 people in the 

study unit rely on private domestic wells for their water supply (Johnson and Belitz, 2017). 

These domestic wells generally are shallower than public drinking-water supply wells in 

the same areas (Shelton and Fram, 2017; Shelton and others, 2013; Burton and others, 

2012). Groundwater quality can vary with depth in aquifer systems; in particular, shallower 

groundwater can be more susceptible to contamination from human activities at the land 

surface.

Land use in the study unit is approximately 72 percent agricultural, 14 percent urban, 

and 14 percent natural, and the largest urban area is the city of Fresno. The dominant crop 

types are orchards and vineyards. Irrigation return flows are the major source of groundwater 

recharge, and pumping for irrigation and municipal supplies is the major source of discharge. 

Previous groundwater studies in this region have identified several water-quality 

constituents of concern in the shallow groundwater resources used by domestic wells, 

including nitrate, uranium, and fumigants (for example, Burow and others, 1999; Jurgens and 

others, 2010; Harter and Lund, 2012).

This study was designed to provide a statistically representative assessment of the 

quality of groundwater resources used for domestic drinking water in the Madera–Chowchilla 

and Kings subbasins. A total of 77 wells were sampled by the GAMA Priority Basin Project 

between August 2013 and April 2014 (Shelton and Fram, 2017). The wells in Madera–

Chowchilla typically were 52 to 122 meters deep, and wells in Kings typically were 35 to 

87 meters deep. Data from 27 domestic wells sampled by the USGS National Water Quality 

Assessment Project between April 2009 and April 2015 also were included in this study.

Overview of Water Quality

The GAMA Priority Basin Project 

evaluates the quality of untreated 

groundwater. Concentrations measured in 

groundwater are compared to benchmarks 

established for drinking-water quality for 

context. A concentration above a benchmark is defined as high (see page 3).

Many inorganic constituents are 

present naturally in groundwater, and their 

concentrations can be affected by natural 

processes and by human activities. About 

21 percent of the groundwater resources 

used for domestic drinking water in 

Madera–Chowchilla, and about 60 percent 

of those in Kings, had high concentrations 

of one or more inorganic constituent. 

Organic constituents are found in 

products used in the home, business, 

industry, and agriculture and can enter the 

environment through normal usage, spills, 

or improper disposal. About 29 percent 

of the groundwater resources used for 

domestic drinking water in Madera–

Chowchilla, and about 20 percent of those 

in Kings, had high concentrations of one or 

more organic constituent.

ISSN 0196-1497 (print)

ISSN 2331-1258 (online)

https://doi.org/10.3133/ofr20171162

CONSTITUENT CONCENTRATIONS

High Moderate Low or not detected

Values are a percentage of the area of the 

groundwater resources used for domestic 

drinking water with concentrations in the 

three specified categories.

Inorganic

constituents

Organic

constituents

Madera–

Chowchilla

60 Kings 28

12

21

41

38

4

20

76

29

3 68

Madera

Fresno

Visalia

Kings

Madera–

Chowchilla

120°30' 120°00' 119°30'

37°

00'

36°

30'

<0.5

0.5 to 5.0

>5.0 to 25.0

>25.0

Population using domestic wells

 in 1990, in persons per square 

 kilometer (modified from 

 Johnson and Belitz, 2017)

Study-unit boundary

Sampled well

EXPLANATION

0 10 20 MILES

0 10 20 KILOMETERS

Base modified from U.S. Geological Survey and other Federal and State digital data, various 

scales; Albers Equal-Area Conic projection, standard parallels are 29°30' N. and 45°30' N.; 

North American Datum of 1983

Map

Area

CALIFORNIA

San

Joaquin

Valley
 

 INORGANIC CONSTITUENTS

RESULTS: Groundwater Quality in the Madera–Chowchilla and Kings Shallow Aquifer Study Unit

Inorganic Constituents with Human-Health Benchmarks

Trace elements are naturally present in the minerals of rocks and sediments and 

in the groundwater that comes into contact with those materials. About 4 percent of 

the groundwater resources used for domestic drinking water in Madera–Chowchilla, 

and about 13 percent in Kings, had high concentrations of one or more trace 

elements. Arsenic and vanadium were present at high concentrations. 

Most of the radioactivity in groundwater comes from the decay of natural 

radioactive isotopes of uranium, thorium, and potassium in minerals in aquifer 

materials. About 9 percent of the groundwater resources used for domestic drinking 

water in Madera–Chowchilla, and about 37 percent in Kings, had high levels of one 

or more radioactive constituent. Uranium, gross alpha-particle activity, and gross 

beta-particle activity were present at high levels. 

Nutrients, including nitrate, are naturally present at low concentrations in 

groundwater, but moderate and high concentrations generally indicate contamination 

from human activities. Common sources of nutrients include fertilizer applied to 

crops and landscaping, seepage from septic systems, and human and animal waste. 

About 13 percent of the groundwater resources used for domestic drinking water 

in Madera–Chowchilla, and about 35 percent in Kings, had high concentrations of 

nitrate.

Inorganic Constituents with Non-Health Benchmarks

(Not included in water-quality overview charts shown on the front page)

Some constituents affect the aesthetic properties of water, such as taste, 

color, and odor, or can create nuisance problems, such as staining and scaling. The 

benchmarks used for these constituents were non-regulatory secondary maximum 

contaminant level benchmarks. 

Total dissolved solids (TDS) concentration is a measure of the salinity of the 

groundwater, and all water naturally contains TDS as a result of the weathering 

and dissolution of minerals in rocks and sediments. The State of California has a 

recommended and an upper limit for TDS in drinking water (see box on page 3). 

About 4 percent of the groundwater resources used for domestic drinking water in 

Madera–Chowchilla, and about 8 percent in Kings, had high concentrations (greater 

than the upper limit) of TDS.

Anoxic conditions (low amounts of dissolved oxygen) can result in the release 

of naturally occurring manganese, iron, and other associated trace elements from 

minerals into groundwater. Manganese or iron was present at high concentrations in 

about 4 percent of the groundwater resources used for domestic drinking water in 

Madera–Chowchilla and about 12 percent in Kings.

Microbial Indicators

(Not included in water-quality overview charts shown on the front page)

Microbial indicators are used to evaluate the potential for fecal contamination 

of water sources. Escherichia coli (E. coli) were not detected in any of the wells 

sampled, and total coliforms were detected in 4 percent of the Madera–Chowchilla 

and 19 percent of the Kings wells sampled. Total coliforms are present naturally 

in soils and in digestive tracts of animals, whereas E. coli specifically indicate 

contamination with animal (or human) fecal waste (California State Water Resources 

Control Board, 2016).

sac16-0631_fig pies

Trace elements

Uranium and radioactive

constituents

Nitrate

Total dissolved solids

Manganese and/or iron

Madera–

Chowchilla Kings

Microbial indicators

81

19

96

4

48

17

35

56 31

13

48

15

37

73

18

9

50 42

8 4

20

76

12 4

93 84

4 3

13

22

65

4

25

71
ORGANIC CONSTITUENTS

RESULTS: Groundwater Quality in the Madera–Chowchilla and Kings Shallow Aquifer Study Unit

Organic Constituents with Human-Health Benchmarks

The Priority Basin Project used laboratory methods that can detect 

concentrations of volatile organic compounds (VOCs) and pesticides that are far 

below human-health benchmarks. VOCs and pesticides detected at these very low 

concentrations can be used to help trace movement of water from the land surface into 

the aquifer system. 

VOCs, including solvents, gasoline components, and refrigerants, are present 

in many household, commercial, and industrial products. VOCs were not detected at 

high concentrations in the groundwater resources used for domestic drinking water in 

Madera–Chowchilla or Kings. The VOC tetrachloroethene (PCE), a commonly used 

solvent, was detected at moderate concentrations in Kings. 

Pesticides, including herbicides, insecticides, and fumigants, are applied to 

crops, gardens, lawns, around buildings, and along roads to help control unwanted 

vegetation, insects, and other pests. Fumigants are VOCs, but are grouped with 

the pesticides because of how they are used. Fumigants are of special interest in 

California because of their historical use to control nematodes in vineyards and 

orchards. 

Fumigant chemicals were present at high concentrations in about 29 percent of 

the groundwater resources used for domestic drinking water in Madera–Chowchilla 

and in about 20 percent in Kings. The fumigant chemicals detected at high concentrations were 1,2-dibromo-3-chloropropane (DBCP), 1,2- dibromoethane (EDB), and 

1,2,3-trichloropropane (1,2,3-TCP). Herbicides and insecticides were not detected at 

high concentrations in the groundwater resources used for domestic drinking water 

in Madera–Chowchilla or Kings. The herbicide simazine was detected at moderate 

concentrations in Madera-Chowchilla.

METHODS FOR EVALUATING GROUNDWATER QUALITY

This study uses comparison to benchmarks established for drinking water 

to provide context for evaluating the quality of groundwater. The quality of 

drinking water may differ from the quality of groundwater because of contact 

with household plumbing, exposure to the atmosphere, or water treatment. 

U.S. Environmental Protection Agency and California State Water Resources 

Control Board Division of Drinking Water regulatory benchmarks set for the 

protection of human health (maximum contaminant level, MCL) are used 

for comparison when available. Otherwise, nonregulatory benchmarks set 

for protection of aesthetic and technical properties, such as taste and odor 

(secondary maximum contaminant level, SMCL) and nonregulatory benchmarks set for the protection of human health (for example, notification levels, 

NL) are used. Water quality in domestic wells is not regulated in California.

Benchmark type and value for selected constituents.

[Benchmarks are listed as EPA (U.S. Environmental Protection Agency) if the EPA and CA (California State Water Resources Control Board Division of Drinking 

Water) values are the same, and as CA if the EPA and CA values are different or if no EPA value exists. MCL, maximum contaminant level; NL, notification level; 

ppm, parts per million (equivalent to milligrams per liter); ppb, parts per billion (equivalent to micrograms per liter); ppt, parts per trillion (equivalent to nanograms 

per liter); pCi/L, picocuries per liter; SMCL, secondary maximum contaminant level]

Constituent Benchmark Constituent Benchmark

Type Value Type Value

Arsenic EPA MCL 10 ppb Manganese EPA SMCL 50 ppb

Vanadium CA NL 50 ppb Iron EPA SMCL 300 ppb

Uranium EPA MCL 30 ppb 1,2-Dibromo-3-chloropropane (DBCP) EPA MCL 0.2 ppb

Gross alpha particle activity EPA MCL 15 pCi/L 1,2-Dibromomethane (EDB) EPA MCL 0.05 ppb

Gross beta particle activity CA MCL 50 pCi/L 1,2,3-Trichloropropane (1,2,3-TCP) CA MCL 5 ppt

Nitrate, as nitrogen EPA MCL 10 ppm 1,2-Dichloropropane EPA MCL 5 ppb

Total dissolved solids (TDS) 

(upper and recommended) CA SMCL 1,000 ppm Trichloroethene EPA MCL 5 ppb

500 ppm Simazine CA MCL 4 ppb

High: Concentrations are greater than the

 benchmark

Moderate: Concentrations are less than

 the benchmark, but greater than one-half 

 (for inorganic constituents) or one-tenth 

 (for organic constituents) the benchmark

Low: Concentrations are less than moderate 

 or the constituent was not detected

Pie diagrams are used to summarize groundwater quality

results. The pie slices represent the percentages of the 

groundwater resources with high, moderate, and low 

concentrations of a constituent. Methods for calculating 

these percentages are discussed by Shelton and others 

(2013) and Burton and others (2012).

sac16-0602_fig pies

VOCs (solvents)

Fumigants

Madera–

Chowchilla Kings

96

4

96

4

78

2

20

71

29

Herbicides

100

100
Factors that Affect Groundwater Quality

The State of California adopted an MCL for 1,2,3-TCP in 2017 (California State Water 

Resources Control Board, 2017). 1,2,3-TCP is used as an industrial solvent and was also present 

as an impurity in some fumigant products. 1,2,3-TCP was detected in about 20 percent of the 

groundwater resources used for domestic drinking water in the Madera–Chowchilla and Kings 

subbasins of the San Joaquin Valley, and all detections were at concentrations greater than the 

MCL of 5 parts per trillion (Shelton and Fram, 2017). 

All samples that had 

detections of 1,2,3-TCP 

also had detections of at 

least one other fumigant 

chemical (DBCP, EDB, or 

1,2-dichloropropane; Shelton 

and Fram, 2017). This pattern 

indicates the source of 1,2,3-

TCP in Madera–Chowchilla 

and Kings groundwater 

resources used for domestic 

supply was likely application of fumigants rather than 

contamination with solvents. 

The use of DBCP, EDB, and 

1,2-dichloropropane as soil 

fumigants was discontinued 

in California by the early 

1980s. The presence of these 

fumigants and associated 

1,2,3-TCP in groundwater 

indicates that at least some of 

the groundwater tapped by domestic wells originated as water at the land surface in areas where 

fumigants were applied approximately 35 to 40 years ago. Concentrations of fumigant chemicals 

in groundwater decrease with time because of chemical degradation of the fumigants and mixing 

with other groundwater that does not contain fumigants (Burow and others, 1999).

Kings

Madera–

Chowchilla

120°30' 120°00' 119°30'

37°

00'

36°

30'

EXPLANATION

Fumigants detected above MCL Fumigants detected below MCL

No fumigants detected

Study-unit boundary

DBCP

1,2,3-TCP

1,2,3-TCP and DBCP

1,2,3-TCP and EDB

0 10 20 MILES

0 10 20 KILOMETERS

Base modified from U.S. Geological Survey and other Federal digital data, various scales; 

Albers Equal-Area Conic projection, standard parallels are 29°30' N. and 45°30' N.;North 

American Datum of 1983

Priority Basin 

Assessments

The GAMA Priority Basin 

Project (PBP) assesses water quality 

in groundwater resources used for 

public and domestic drinking-water 

supplies. This study in the Madera–

Chowchilla and Kings subbasins 

of the San Joaquin Valley focused 

on groundwater resources used for 

domestic drinking water. Ongoing 

assessments are being carried out in 

more than 120 basins and in hard-rock 

aquifers outside of basins throughout 

California. The PBP assessments 

compare constituent concentrations 

in untreated groundwater with 

benchmarks established for the 

protection of human health and for 

aesthetic concerns. The PBP does not 

evaluate the quality of drinking water.

The PBP uses two scientific 

approaches for assessing groundwater 

quality. The first approach uses a 

network of wells to statistically assess 

the status of groundwater quality. The 

second approach combines waterquality, hydrologic, geographic, 

and other data to help assess the 

factors that affect water quality. The 

PBP includes chemical analyses 

not generally available as part of 

regulatory compliance monitoring, 

including measurements at 

concentrations much less than humanhealth benchmarks and measurement 

of constituents that can be used to 

trace the sources and movement of 

groundwater.

For more information

Technical reports and hydrologic data 

collected for the GAMA Program may 

be obtained from:

GAMA Project Chief

U.S. Geological Survey

California Water Science Center

6000 J Street, Placer Hall

Sacramento, CA 95819

Telephone number: (916) 278-3000

WEB: http://ca.water.usgs.gov/gama

GAMA Program Unit Chief

State Water Resources Control Board

Division of Water Quality 

PO Box 2231, Sacramento, CA 95812

Telephone number: (916) 341-5779

WEB: 

http://www.waterboards.ca.gov/gama

ISSN 2327-6916 (print)

ISSN 2327-6932 (online)

http://dx.doi.org/10.3133/fsxxxxxxxx

By Miranda S. Fram and Jennifer L. Shelton

REFERENCES CITED

Burow, K.R., Panshin, S.Y., Dubrovsky, N.M., VanBrocklin, D., and Fogg, G.E., 1999, Evaluation of processes 

affecting 1,2-dibromo-3-chloropropane (DBCP) concentrations in groundwater in the eastern San Joaquin 

Valley: Analysis of chemical data and groundwater flow and transport simulations: U.S. Geological Survey 

Water-Resources Investigations Report 99–4059, 57 p., https://pubs.er.usgs.gov/publication/wri994059. 

Burton, C.A., Shelton, J.L., and Belitz, K., 2012, Status and understanding of groundwater quality in the two 

southern San Joaquin Valley study units, 2005–2006—California GAMA Priority Basin Project: U.S. Geological Survey Scientific Investigations Report 2011–5218, 150 p., https://pubs.usgs.gov/sir/2011/5218/.

California State Water Resources Control Board, 2016, Groundwater Information Sheet: Bacterial Indicators, 

http://www.waterboards.ca.gov/gama/docs/coc_bacteria_indicators.pdf.

California State Water Resources Control Board, 2017, 1,2,3-Trichloropropane maximum contaminant level, 

https://www.waterboards.ca.gov/drinking_water/certlic/drinkingwater/123TCP_SBDDW-17-001.

Harter, T., and Lund, J.R., 2012, Addressing nitrate in California’s drinking water with a focus on Tulare Lake 

Basin and Salinas Valley groundwater: University of California, Davis, Center for Watershed Sciences, 78 

p., http://groundwaternitrate.ucdavis.edu/. 

Johnson, T.D., and Belitz, K., 2017, Domestic well locations and populations served in the contiguous U.S., 1990: Science of the Total Environment, v. 607–608, p. 658–668, https://doi.org/10.1016/j.

scitotenv.2017.07.018.

Jurgens, B.C., Fram, M.S., Belitz, K., Burow, K.R., and Landon, M.K., 2010, Effects of groundwater development on uranium: Central Valley, California, USA: Ground Water, v. 48, p. 913–928, 

http://dx.doi.org/10.1111/j.1745-6584.2009.00635.x.

Shelton, J.L., and Fram, M.S., 2017, Groundwater-quality data for the Madera/Chowchilla–Kings shallow aquifer study unit, 2013–14: Results from the California GAMA Program: U.S. Geological Survey Data Series 

1019, 115 p., https://doi.org/10.3133/ds1019.

Shelton, J.L., Fram, M.S., Belitz, K., and Jurgens, B.C., 2013, Status and understanding of groundwater quality 

in the Madera-Chowchilla Study Unit, 2008—California GAMA Priority Basin Project: U.S. Geological 

Survey Scientific Investigations Report 2012–5094, 86 p., https://pubs.usgs.gov/sir/2012/5094/.