U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2012–3111

March 2013 Printed on recycled paper

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

Groundwater Quality in the San Francisco Bay 

Groundwater Basins, 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 groundwater quality and increases public access to groundwater-quality information. Selected 

groundwater basins of the San Francisco Bay area constitute one of the study units being evaluated.

Shaded relief derived from

U.S. Geological Survey 

National Elevation Dataset, 2006, 

Albers Equal Area Conic Projection

SAN FRANCISCO CO

ALAMEDA CO

SANTA CRUZ CO

CONTRA COSTA CO

MARIN CO

SAN MATEO CO

SANTA CLARA VALLEY

SANTA CLARA CO

Hayward

Alameda

Oakland

San Francisco

San Jose

San Mateo

Palo Alto

Santa Clara

Sunnyvale

Fremont

Morgan Hill

Arroyo Calero

Arroyo Valle

Guadalupe River

Arroyo Hondo

Llagas Creek

Arroyo de la Laguna

Arroyo Valle

Coyote Creek

Diablo Range

Contra Costa Canal

Dutch Slough

P a c i f i c O c e a n

San Francisco

Bay

Golden Gate Strait

0 10 20 MILES

0 10 20 KILOMETERS

EXPLANATION

Groundwater basins in the

 San Francisco Bay Study Unit

Downtown

Islais Valley

Lobos

Marina

South San Francisco

Visitacion Valley

Westside

Santa Clara Valley

Organic

constituents

Inorganic

constituents

High Moderate

CONSTITUENT CONCENTRATIONS

Low or not detected 

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

with concentrations in the three specified categories. Values on

piechart may not equal 100 due to rounding of percentages.

<1

88

5

25

70

12

The San Francisco Bay Study Unit

The San Francisco Bay study unit is approximately 620 square miles and consists 

of the Marina, Lobos, Downtown, Islais Valley, South San Francisco, Visitacion Valley, 

Westside, and the Santa Clara Valley groundwater basins (California Department of Water 

Resources, 2003). These basins were grouped into one study area primarily on the basis of 

geography (Ray and others, 2009). 

The study unit has warm, dry summers and cool, moist winters. Average yearly rainfall across the study unit ranges from 14 inches (in.) in the southern and southwestern parts 

of the study unit to 

28 in. in the north. 

The study unit is 

drained primarily 

by the Guadalupe 

River, the Coyote 

Creek, and their 

principal tributaries. The primary 

aquifer system 

consists of alluvial 

sediments (mixtures of sand, silt, 

clay, and gravel), 

fluvial deposits, and marine 

estuarine deposits 

(locally referred to 

as the “Bay Mud”). 

For this study, the 

primary aquifer 

system is defined as 

the part of the aquifer corresponding 

to the perforated 

intervals of publicsupply wells listed 

in the California 

Department of Public Health database. Public-supply wells are typically drilled to depths 

between 200 and 700 feet, consist of solid casing from the land surface to a depth of about 

175 to 425 feet, and are perforated below the solid casing. Water quality in the shallower 

and deeper parts of the aquifer system may differ from that in the primary aquifer system.

Land use in the study unit is approximately 77 percent (%) urban, 22% natural, and 

1% agricultural. The largest urban areas are the cities of San Francisco, San Jose, Santa 

Clara, Sunnyvale, Fremont, and Oakland. Natural lands are mostly grassland.

Recharge to groundwater occurs primarily from infiltration of imported water, 

mountain-front recharge, streamflow, infiltration of water from precipitation and irrigation, and leakage from transmission pipelines. The primary sources of discharge are water 

pumped for irrigation and municipal supply, evaporation, and discharge to streams and the 

San Francisco Bay.

Overview of Water Quality

GAMA’s Priority Basin Project 

evaluates the quality of untreated groundwater. However, for context, benchmarks 

established for drinking-water 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 the inorganic constituents can be 

affected by natural processes as well as 

by human activities. In the San Francisco 

Bay study unit, one or more inorganic 

constituents were present at high concentrations in about 5% of the primary aquifer 

system and at moderate concentrations in 

about 25%.

Human-made organic constituents 

are found 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 less than 1% of 

the primary aquifer system and at moderate concentrations in about 12%.
 

Trace and

minor elements 

Salinity

indicators

Nutrients

Uranium and

radioactive

constituents

Iron or

manganese

Perchlorate

INORGANIC CONSTITUENTS

SPECIAL-INTEREST CONSTITUENT

3 3

94

76

42

58

12

12

99

2

79

19

7

37 56

<1

RESULTS: Groundwater Quality in the San Francisco Bay Study Unit

Inorganic Constituents with Human-Health Benchmarks

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

and in the water that comes into contact with those materials. In the San Francisco 

Bay study unit, barium was the only trace element detected at high concentrations (in 

about 3% of the primary aquifer system). 

Radioactivity is the release of energy or energetic particles during spontaneous 

decay of unstable atoms. Most of the radioactivity in groundwater comes from the 

decay of naturally occurring isotopes of uranium and thorium in minerals in the sediments of the aquifer. Radioactive constituents were not detected at high concentrations in the primary aquifer system, and were detected at moderate concentrations in 

<1% based on the spatially weighted approach.

Nutrients, such as nitrate and nitrite, can be naturally present at low concentrations in groundwater. High and moderate concentrations generally occur as a result 

of human activities, such as applying fertilizer to crops. Livestock, when in concentrated numbers, and septic systems also produce nitrogenous waste that can leach 

into groundwater. Nutrients were present at high concentrations in about 2% of the 

primary aquifer system and at moderate concentrations in about 19% of the primary 

aquifer system.

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 scaling and staining. The State 

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

in drinking water. All groundwater naturally contains TDS as a result of the weathering and dissolution of minerals in the sediments. Anoxic conditions in groundwater 

(low amounts of dissolved oxygen) may result in release of manganese and iron from 

minerals into groundwater.

In the San Francisco Bay study unit, salinity indicator concentrations (TDS and/

or chloride) were high in about 7% of the primary aquifer system. About 37% of the 

primary aquifer system had moderate concentrations of salinity indicators. Iron and 

manganese are naturally occurring elements, and they were present (one or both) 

at high concentrations in about 12% of the primary aquifer system and at moderate 

concentrations in about 12% of the primary aquifer system.

Perchlorate 

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

Perchlorate is an inorganic constituent which has been regulated in California 

drinking water since 2007. It is an ingredient in rocket fuel, fireworks, and other 

products, may be present in some fertilizers, and occurs at low concentrations under 

natural conditions in groundwater. Perchlorate was not detected at high concentrations in the primary aquifer system and was detected at moderate concentrations in 42%. 
High concentrations

Moderate concentrations

Low concentrations

or not detected

EX

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

with concentrations in the three specified categories. Values

on pie chart may not equal 100 due to rounding of percentages.

CONSTITUENT CONCENTRATIONS

Solvents

Other

VOCs

ORGANIC CONSTITUENTS

Herbicides

Trihalomethanes

95

5 <1

98

2

98

98

2

2

<1

RESULTS: Groundwater Quality in the San Francisco Bay Study Unit

Organic Constituents

The Priority Basin Project uses laboratory methods that can detect low concentrations of volatile organic compounds (VOCs) and pesticides, far below human-health 

benchmarks. The presence of VOCs and pesticides detected at these low concentrations can be used to trace water from the landscape into the aquifer system.

Volatile Organic Compounds with Human-Health Benchmarks

VOCs are used 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 San Francisco Bay study unit, solvents were present at high concentrations 

in less than (<) 1% of the primary aquifer system. The solvent detected at high concentrations was tetrachloroethene. Solvents were detected at moderate concentrations 

(mainly tetrachloroethene and trichloroethene) in about 5% of the primary aquifer 

system.

Trihalomethanes may form during municipal water purification and can enter 

groundwater by the infiltration of landscape irrigation water. Trihalomethanes were 

detected at moderate concentrations in about 2% of the primary aquifer system.

Other VOCs include organic synthesis reagents and gasoline additives. 

Other VOCs were detected at high concentrations in <1% of the primary aquifer 

system and at moderate concentrations in about 2% of the primary aquifer system. The compound detected at high concentrations was the gasoline additive 

methyl tert-butyl ether (MTBE). 

Pesticides with Human-Health Benchmarks

Pesticides are applied to crops, gardens, lawns, around buildings, and along roads 

to help control unwanted vegetation (weeds), insects, fungi, and other pests. In the San 

Francisco Bay study unit, insecticides (including fumigants) were not detected at high 

or moderate concentrations in the primary aquifer system. Herbicides were detected at 

moderate concentrations in about 2% of the primary aquifer system, reflecting moderate concentrations of atrazine.

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 for the evaluation 

when available. Otherwise, non-regulatory benchmarks for protecting aesthetic properties 

(Secondary Maximum Contaminant Level, SMCL), such as taste and odor, and nonregulatory 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 includes nondetections and values less than moderate concentrations. Methods for evaluating water quality are discussed in Parsons and others (2013).
SAN FRANCISCO CO

ALAMEDA CO

SANTA CRUZ CO

CONTRA COSTA CO

MARIN CO

SAN MATEO CO

SANTA CLARA

VALLEY

SANTA CLARA CO

Arroyo Valle

Guadalupe

 River

Arroyo Hondo

Arroyo de la Laguna

Coyote 

Diablo Range

Santa Ceuz Mts

P a c i f i c O c e a n

San Francisco

Bay

Golden Gate Strait

0 10 20 MILES

0 10 20 KILOMETERS

San Andreas Fault

Hayward Fault

Atherton

TOTAL DISSOLVED SOLIDS

CONCENTRATION, IN

MILLIGRAMS PER LITER

USGS- or CDPH-grid well 

USGS-understanding well 

CDPH-other well

Less than 500

Less than 500

501 to 1,000 

501 to 1,000 

Greater than 1,000

Less than 500

501 to 1,000 

Creek

Quaternary

Tertiary

Quaternary

Tertiary

Cretaceous

Water

EXPLANATION

GEOLOGIC UNIT

Sedimentary rocks Sedimentary and

 metasedimentary

 rocks

Plutonic, metavolcanic,

 and mixed rocks

Cenozoic Mesozoic

Volcanic rocks

Plio-Pleistocene

 sediment

Mafic volcanics

Quaternary alluvium

Quaternary other

 sediment

Marine sediment

Nonmarine sediment

Mafic volcanics

Franciscan

 complex

Granitic rocks

Metamorphic

 other

Metasediment

Pyroclastic volcanics

Ultramafic/

 mafic

Niles Cone

sub-basin

Salinity in the San Francisco Bay Study Unit

In the San Francisco Bay study unit, inorganic constituents with health-based benchmarks—trace elements, nutrients, and radioactive constituents—are present at high concentrations in about 5% of the primary aquifer system. In contrast, in most areas investigated by 

the GAMA Priority Basin Project, inorganic constituents are present at high concentrations in 

10 to 25% of the primary aquifer system. The constituent present at high concentrations in the 

greatest proportion of the primary aquifer system was TDS, which is an indicator of salinity that has an SMCL (an aesthetic-based benchmark). In California, the SMCL for TDS is 

1,000 milligrams per liter (mg/L), whereas the U.S. Environmental Protection Agency SMCL 

for TDS is 500 mg/L. TDS was present at high concentrations (greater than 1,000 mg/L) in 

7% of the primary 

aquifer system and at 

moderate concentrations (between 500 

and 1,000 mg/L) 

in 37%. 

Natural sources 

of TDS to groundwater in the San 

Francisco Bay study 

unit include saltwater 

intrusion from the 

Bay and interaction 

between recharge 

water and aquifer 

materials derived 

from marine or 

estuarine sediments. 

On the east side of 

the Bay, high and 

moderate concentrations of TDS were 

detected in areas 

with a history of 

intrusion of water 

from the Bay in 

response to pumping of freshwater from aquifers. Continuous pumping in the Niles Cone subbasin allowed these saline waters to migrate from the shallow aquifers through the Bay Mud 

to deeper aquifers used for public supply (Figuers, 1998). On the southwest side of the Bay, 

moderate concentrations of TDS occur on an alluvial fan near the town of Atherton. Upwelling of connate saline water from marine sediments may be a source of TDS to these aquifers 

(Metzger and Fio, 1997). On the east side of the Santa Clara Valley, moderate concentrations 

of TDS occur in wells along Coyote Creek, which drains marine sediments in the Diablo 

Range to the east of the study unit and also receives water from various impoundments in the 

southern part of the valley for groundwater recharge. Accumulation of salts in Coyote Creek 

along the flowpath from both of these waters may be a source of TDS to the aquifers.

SELECTED REFERENCES

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

Resources Bulletin 118, 246 p., accessed September 7, 2012, at http://www.water.ca.gov/groundwater/

bulletin118/update2003.cfm. 

Figuers, S., 1998, Groundwater study and water supply history of the East Bay Plain, Alameda and Contra 

Costa Counties, CA: Norfleet Consultants Project Number 971102, 90 p., accessed September 7, 2012, at 

http://www.waterboards.ca.gov/sanfranciscobay/water_issues/programs/groundwater/GW_East_Bay_Plain_

report_and_color_figures.pdf.

Metzger, L.F., and Fio, J.L., 1997, Ground-water development and the effects on ground-water levels and water 

quality in the town of Atherton, San Mateo County, California: U.S. Geological Survey Water-Resources 

Investigations Report 97-4033, 31 p. (Also available at http://pubs.usgs.gov/wri/1997/4033/report.pdf.)

Parsons, M.C., Kulongoski, J.T., and Belitz, Kenneth, 2013, Status and understanding of groundwater quality in the San Francisco Bay groundwater basins, 2007—California GAMA Priority Basin Project: U.S. 

Geological Survey Scientific Investigations Report 2012-5248, 74 p. (Also available at http://pubs.usgs.gov/

sir/2012/5248.)

Ray, M.C., Kulongoski, J.T., and Belitz, Kenneth, 2009, Ground-water quality data in the San Francisco Bay 

study unit, 2007—Results from the California GAMA Program: U.S. Geological Survey Data Series 396, 

92 p. (Also available at http://pubs.usgs.gov/ds/396.)

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 water quality in shallower and deeper parts of the aquifers. GAMA’s Domestic Well Project 

assesses water quality in the shallower 

parts of the aquifer system. Ongoing 

PBP 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 waterquality, hydrologic, geographic, and 

other data to help assess the factors 

that affect water quality. In the San 

Francisco Bay study unit, data were 

collected by the PBP in 2007 and from 

the CDPH database for 2004–2007. 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 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/

By Mary C. Parsons (formerly Mary C. Ray), Justin T. Kulongoski, and

Kenneth Belitz