Fact Sheet 2012–3099 

January 2013

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

Groundwater Quality in the Madera and Chowchilla 

Subbasins of the 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 Priority Basin 

Project of the GAMA Program provides a comprehensive assessment of the State’s untreated groundwater quality 

and increases public access to groundwater-quality information. The Madera and Chowchilla subbasins of the San 

Joaquin Valley constitute one of the study units being evaluated.

Organic 

Constituents

Inorganic 

Constituents

High Moderate

CONSTITUENT CONCENTRATIONS

Low or not detected 

Pie charts illustrate the proportion of the primary aquifer 

system with concentrations in specified categories. 

33 37

30 87

3

10

Printed on recycled paper

The Madera-Chowchilla Study Unit

The Madera-Chowchilla study unit is about 860 square miles and consists of the 

Madera and Chowchilla groundwater subbasins of the San Joaquin Valley Basin (California Department of Water Resources, 2003; Shelton and others, 2009). The study unit 

has hot, dry summers and cool, moist winters. Average annual rainfall ranges from 11 

to 15 inches, most of which occurs between November and February. The main surfacewater features in the study unit are the San Joaquin, Fresno, and Chowchilla Rivers, 

and the Madera and Chowchilla canals. Land use in the study unit is about 69 percent 

(%) agricultural, 28% natural (mainly grasslands), and 3% urban. The primary crops are 

orchards and vineyards. The largest urban area is the city of Madera. 

The primary aquifer system is 

defined as those parts of the aquifer 

corresponding to the perforated intervals 

of wells listed in the California Department of Public Health (CDPH) database. 

In the Madera-Chowchilla study unit, 

these wells typically are drilled to depths 

between 200 and 800 feet, consist of 

a solid casing from land surface to a 

depth of about 140 to 400 feet, and are 

perforated below the solid casing. Water 

quality in the primary aquifer system 

may differ from that in the shallower and 

deeper parts of the aquifer system. 

The primary aquifer system in the study unit consists of Quaternary-age alluvial-fan 

and fluvial deposits that were formed by the rivers draining the Sierra Nevada. Sediments consist of gravels, sands, silts, and clays and generally are coarser closest to the 

Sierra Nevada and become finer towards the center of the basin. The structure and composition of the deposits in the Madera-Chowchilla study unit are different from those in 

other parts of the eastern San Joaquin Valley because the Fresno and Chowchilla Rivers 

primarily drain the Sierra Nevada foothills, whereas the larger rivers drain higher elevations with greater sediment supply. These differences in the sources of sediments are 

important because they may affect the groundwater chemistry and the physical structure 

of the sedimentary deposits. Some of the clay layers are lacustrine deposits, the most 

extensive of which, the Corcoran Clay, underlies the western part of the study unit and 

divides the primary aquifer system into an unconfined to semi-confined upper system 

and a largely confined lower system.

Regional lateral flow of groundwater is southwest towards the valley trough. 

Irrigation return flows are the major source of groundwater recharge, and groundwater 

pumping is the major source of discharge. Groundwater on a lateral flow path may be 

repeatedly extracted by pumping wells and reapplied at the surface multiple times before 

reaching the valley trough, resulting in a substantial component of downward vertical 

flow (Burow and others, 2004; Phillips and others, 2007; Faunt, 2009). This flow pattern 

enhances movement of water from shallow depths to the primary aquifer system.

Overview of Water Quality

GAMA’s Priority Basin Project 

evaluates the quality of untreated 

groundwater. However, for context, 

benchmarks established for drinkingwater quality are used for comparison. 

Benchmarks and definitions of high, 

moderate, and low concentrations are 

discussed in the inset box on page 3.

Many inorganic constituents 

occur naturally in groundwater. The 

concentrations of inorganic constituents 

can be affected by natural processes 

as well as by human activities. In the 

Madera-Chowchilla study unit, one 

or more inorganic constituents were 

present at high concentrations in about 

37% of the primary aquifer system and 

at moderate concentrations in about 

30%.

Human-made organic constituents 

are present in products used in 

the home, business, industry, and 

agriculture. Organic constituents can 

enter the environment through normal 

usage, spills, or improper disposal. In 

this study unit, one or more organic 

constituents were present at high 

concentrations in about 10% of the 

primary aquifer system and at moderate 

concentrations in about 3%.

SIERRA NEVADA

Madera

Subbasin

Eastern boundary of Corcoran Clay

in subsurface

Chowchilla

Subbasin

MERCED CO.

FRESNO CO.

MARIPOSA CO.

MADERA CO.

Madera

Chowchilla

Madera

Subbasin

Eastern boundary of Corcoran Clay

in subsurface

Chowchilla

Subbasin

MERCED CO.

FRESNO CO.

MARIPOSA CO.

MADERA CO.

Madera

ChowchillaChowchillaChowchilla

0 5 10 MILES

0 10 KILOMETERS 5

"

"

Chowchilla River Chowchilla River

San Joaquin River San Joaquin River

San Joaquin RiverSan Joaquin River

CHOWCHILLA CANALCHOWCHILLA CANAL

MADERA CANALMADERA CANAL

Fresno RiverFresno River

Hensley Lake

H.V. Eastman Lake

Millerton Lake

U.S. Department of the Interior

U.S. Geological Survey
 

 

RESULTS: Groundwater Quality in the Madera-Chowchilla Study Unit

Inorganic Constituents with Human-Health Benchmarks

Trace elements are naturally present in the minerals in rocks and soils, and in the 

water that comes into contact with those materials. In the Madera-Chowchilla study 

unit, one or more trace elements were present at high concentrations in about 13% of 

the primary aquifer system, and at moderate concentrations in about 30%. Arsenic and 

vanadium were the trace elements that most frequently occurred at high concentrations, in about 13% and about 3% of the primary aquifer system, respectively. Barium 

and strontium also were detected at high concentrations, but only in less than 2% of the 

primary aquifer system. 

Radioactivity is the emission of energy or energetic particles during spontaneous 

decay of unstable atoms. Humans are exposed to small amounts of natural radioactivity every day. Most of the radioactivity in groundwater comes from decay of naturally 

occurring uranium and thorium in minerals in the sediments of the aquifer. In the 

Madera-Chowchilla study unit, radioactive constituents occurred at high levels in about 

20% of the primary aquifer system, and at moderate levels in about 3%. Gross alpha 

particle activity and uranium activity were the radioactive constituents that most frequently occurred at high levels.

Nutrients, such as nitrogen, are naturally present at low concentrations in groundwater. High and moderate concentrations generally occur as a result of human activities. Common sources of nutrients include fertilizers applied to crops and landscaping, 

seepage from septic systems, and human and animal waste. In the Madera-Chowchilla 

study unit, nitrate was present at high concentrations in about 7% of the primary aquifer 

system and at moderate concentrations in about 20%.

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 may create nuisance problems, such as staining and scaling. The State of 

California has a recommended and an upper limit for total dissolved solids (TDS) in 

drinking water. Groundwater naturally contains TDS as a result of the weathering and 

dissolution of minerals in soils. In the Madera-Chowchilla study unit, TDS was present 

at high concentrations (greater than the upper limit) in about 7% of the primary aquifer 

system, and at moderate concentrations (between the recommended and upper limit) in 

about 13%. 

Manganese occurs naturally in minerals, and anoxic conditions (low amounts of 

dissolved oxygen) in groundwater may result in the release of manganese from minerals 

into groundwater. Manganese was present at high concentrations and moderate concentrations, each, in about 3% of the primary aquifer system.

Perchlorate

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

Perchlorate is an inorganic constituent that has been regulated in California drinking water since 2007. It is an ingredient in rocket fuel, fireworks, safety flares, and some 

fertilizers, and also occurs naturally at low concentrations in groundwater. In the MaderaChowchilla study unit, perchlorate was not detected at high concentrations in the primary 

aquifer system but was detected at moderate concentrations in about 20% of the primary 

aquifer system.

Trace 

Elements

Total 

Dissolved 

Solids

Radioactive

Constituents

Nutrients

Manganese

Perchlorate

INORGANIC CONSTITUENTS

INORGANIC CONSTITUENTS SPECIAL-INTEREST CONSTITUENT

13

77

7

7

20

73

20

80

80

94

3

3 3

20

13

57 30
High 

Moderate

EX

Low or not detected

AMPLE Values are a percentage of the area of the primary aquifer 

system with concentrations in the three specified categories.

CONSTITUENT CONCENTRATIONS

RESULTS: Groundwater Quality in the Madera-Chowchilla Study Unit

Organic Constituents

The Priority Basin Project uses laboratory methods that can detect the presence 

of volatile organic compounds (VOCs) and pesticides at low concentrations, far below 

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

can be used to help trace water pathways from the landscape into the aquifer system.

Volatile Organic Compounds with Human-Health Benchmarks

VOCs are in many household, commercial, industrial, and agricultural products 

and are characterized by their tendency to volatilize (evaporate) into the air. Solvents 

are used for a number of purposes, including manufacturing and cleaning. In the 

Madera-Chowchilla study unit, solvents were not present at high concentrations in the 

primary aquifer system. Solvents were present at moderate concentrations in about 3% 

of the primary aquifer system and at low concentrations (or not detected) in about 97%. 

Other VOCs include trihalomethanes, gasoline additives, refrigerants, and organic 

synthesis reagents. Other VOCs were not detected at high or moderate concentrations 

in the primary aquifer system, and trihalomethanes were detected at low concentrations. Trihalomethanes can form during disinfection of water supplies and may enter 

groundwater by the infiltration of landscape irrigation water, leakage from septic and 

sewage systems, or use of disinfection solutions in wells. Fumigants, a class of VOCs in 

agricultural products and a type of pesticide, are discussed with pesticides.

Pesticides with Human-Health Benchmarks

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

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

(weeds), insects, fungi, and other pests. Fumigants are of special interest in California 

because of their historical use to control nematodes in vineyards and orchards.

In the Madera-Chowchilla study unit, fumigants were present at high concentrations in about 10% of the primary aquifer system, and at moderate concentrations in 

0.2%. The fumigant detected at high concentrations was 1,2-dibromo-3-chloropropane 

(DBCP). DBCP was not detected at moderate or low concentrations. The use of DBCP 

as a soil fumigant was discontinued in California in 1977. Herbicides were not detected 

at high or moderate concentrations in the primary aquifer system, but were frequently 

detected at low concentrations. Insecticides that are not fumigants were not detected.

BENCHMARKS FOR EVALUATING GROUNDWATER QUALITY

 GAMA’s Priority Basin Project uses benchmarks established for drinking water 

to provide context for evaluating the quality of untreated groundwater. After withdrawal, groundwater may be disinfected, filtered, mixed, and exposed to the atmosphere 

before being delivered to consumers. Federal and California regulatory benchmarks for 

protecting human health (Maximum Contaminant Level, MCL) were used when available. Otherwise, non-regulatory benchmarks for protecting aesthetic properties, such as 

taste and odor (Secondary Maximum Contaminant Level, SMCL), and non-regulatory 

benchmarks for protecting human health (Notification Level, NL, and Lifetime Health 

Advisory, HAL) were used.

High, moderate, and low concentrations are defined relative to benchmarks

Concentrations are considered high if they are greater than a benchmark. For inorganic constituents, concentrations are moderate if they are greater than one-half of a benchmark. For organic and special-interest constituents, concentrations are moderate if they 

are greater than one-tenth of a benchmark; this lower threshold was used because organic constituents generally are less prevalent and 

have smaller concentrations relative to benchmarks than inorganic constituents. Low concentrations include nondetections and values 

less than moderate concentrations. Methods for evaluating water quality are discussed by Shelton and others (2012).

Solvents

Herbicides

Fumigants

Other Volatile 

Organic 

Compounds

ORGANIC CONSTITUENTS

0.2

3

97

100

100

90

10
0

100

200

300

400

500

600

Depth to top of perforations,

in feet below land surface

0 10 20 30 40 50 20 4 6 8 10 12 0 5 10 15 20 25

Uranium, in picocuries per liter Nitrate-n, in milligrams per liter Arsenic, in micrograms per liter

For URANIUM and NITRATE graphs

Location relative to Corcoran Clay

For ARSENIC graph

Distance from Chowchilla River

East Below Above or

across

less than

5 miles

more than

5 miles

Modern

Mixed

Pre-modern

Groundwater

Age

Constituent 

concentrations

High

Moderate

Low

Factors that Affect Groundwater Quality

In the Madera-Chowchilla study unit, uranium (17%), arsenic (13%), and nitrate 

(7%) were the inorganic constituents that were most frequently detected at high concentrations in the primary aquifer system. High and moderate concentrations of uranium 

and nitrate were found in shallower wells (depth to top of well perforations less than 

235 feet), and in wells located in the western part of the study unit above the Corcoran 

Clay. Groundwater with elevated concentrations of uranium and nitrate was classified 

predominantly as modern or mixed age. Tritium and carbon-14 dating were used to 

define groundwater age: modern, recharged since 1950; pre-modern, recharged before 

1950; and mixed, containing modern and pre-modern waters. Jurgens and others (2009) 

showed that downward-moving irrigation-return water that recharges aquifers in the 

Eastern San Joaquin Valley contains high concentrations of bicarbonate. The bicarbonate dissolves naturally occurring uranium off of the sediments, and recharge transports 

the uranium to the depths of the primary aquifer system. Nitrate derived from human 

activities on the land surface would also be transported into the primary aquifer system 

by this recharge process.

By Jennifer L. Shelton, Miranda S. Fram, and Kenneth Belitz

REFERENCES

Burow, K.R., Shelton, J.L., Hevesi, J.A., and Weissmann, G.S., 2004, Hydrogeologic characterization 

of the Modesto area, San Joaquin Valley, California: U.S. Geological Survey Scientific 

Investigations Report 2004-5232, 54 p.

California Department of Water Resources, 2003, California’s groundwater: California Department 

of Water Resources Bulletin 118, 246 p., accessed July 1, 2011, at http://www.water.ca.gov/

groundwater/bulletin118/update2003.cfm/

Faunt, C.C., ed., 2009, Groundwater availability of the Central Valley aquifer, California: U.S. 

Geological Survey Professional Paper 1766, 225 p. 

Jurgens, B.C., Fram, M.S., Belitz, K., Burow, K.R., and Landon, M.K., 2009, Effects of groundwater 

development on uranium—Central Valley, California, USA: Ground Water, v. 48, no. 6, 

p. 913–928.

Phillips, S.P., Green, C.T., Burow, K.R., Shelton, J.L., and Rewis, D.L., 2007, Simulation of 

multiscale ground-water flow in part of the northeastern San Joaquin Valley, California: U.S. 

Geological Survey Scientific Investigations Report 2007-5009, 43 p.

Shelton, J.L., Fram, M.S., and Belitz, K., 2009, Groundwater-quality data for the Madera-Chowchilla 

study unit, 2008—Results from the California GAMA Program: U.S. Geological Survey Data 

Series 455, 80 p. (Also available at http://pubs.usgs.gov/ds/455/.)

Shelton, J.L., Fram, M.S., Belitz, K., and Jurgens, B.C., 2012, Status and understanding of 

groundwater quality in the Madera-Chowchilla study unit, 2008: U.S. Geological Survey 

Scientific Investigations Report 2012-5094, 86 p. (Also available at http://pubs.usgs.gov/

sir/2012/5094.)

Priority Basin Assessments 

GAMA’s Priority Basin Project 

(PBP) assesses water quality in that part 

of the aquifer system used for drinking 

water, primarily public supply. Water 

quality in the primary aquifer system 

may differ from that in the deep parts 

of the aquifer, or from that in the shallower parts, which are being assessed by 

GAMA’s Domestic Well Project. Ongoing assessments are being conducted 

in more than 120 basins throughout 

California. 

The PBP assessments are based on 

a comparison of 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 delivered to 

consumers. 

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 water-quality, 

hydrologic, geographic, and other data to 

help assess the factors that affect water 

quality. In the Madera-Chowchilla study 

unit, data were collected by the PBP in 

2008 and from the CDPH database for 

2005–2008. The PBP includes chemical 

analyses not generally available as part 

of regulatory compliance monitoring, 

including measurements at concentrations much lower than human-health 

benchmarks and measurements 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

4165 Spruance Road, Suite 200

San Diego, CA 92101

Telephone number: (619) 225-6100

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

GAMA Program Unit

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

In contrast, high and moderate concentrations of arsenic were detected in deeper 

wells (depth to top of well perforations greater than 235 feet), and in groundwater 

classified as pre-modern or mixed age. Most of the moderate and high arsenic concentrations were in wells located within 5 miles of the Chowchilla River. Sediments along 

the Chowchilla River likely are different from those along the Fresno and 

San Joaquin Rivers.