U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2010–3060

September 2010 Printed on recycled paper

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

Groundwater Quality in the North 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. The basins 

north of San Francisco constitute one of the study units being evaluated. 

The North San Francisco Bay Study Unit

The North San Francisco Bay study unit is approximately 1,000 square miles and 

consists of the Wilson Grove Formation Highlands, Alexander Valley, Santa Rosa Valley, 

Petaluma Valley, Lower Russian River Valley, Kenwood Valley, Volcanic Highlands, and 

Napa-Sonoma Valley groundwater basins (California Department of Water Resources, 

2003). These basins were grouped into three study areas primarily on the basis of geology. 

The alluvium-filled valleys were combined to form the Valleys and Plains study area; the 

Wilson Grove Formation Highlands and the Volcanic Highlands were designated as the 

other two study areas (Kulongoski and others, 2006). 

The study unit has warm, dry summers and cool, moist winters. Average annual 

rainfall is 30 inches. The study areas are drained by several rivers and their principal 

tributaries. The primary aquifers consist of alluvial sediments (mixtures of sand, silt, clay, 

cobbles, and boulders), marine deposits (fossiliferous sandstones containing lenses of conglomerate and sandy shale), and volcanic deposits (pumice tuff, tuff breccias). The primary 

aquifers are defined as those 

parts of the aquifers corresponding to the perforated 

intervals of wells listed in 

the California Department 

of Public Health database. 

Public-supply wells are 

typically drilled to depths 

between 200 and 500 feet, 

consist of solid casing from 

the land surface to a depth of 

about 60 to 200 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 

aquifers.

Land use in the study 

unit is approximately 55 

percent (%) natural (mostly 

grasslands and forests), 31% 

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 the inorganic constituents can 

be affected by natural processes as well 

as by human activities. In the North San 

Francisco Bay study unit, one or more 

inorganic constituents were present at 

high concentrations in about 14% of 

the primary aquifers and at moderate 

concentrations in about 36%.

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 about 1% 

of the primary aquifers and at moderate 

concentrations in about 5%.

agricultural, and 14% urban. The primary agricultural uses are for pasture, hay, vineyards, 

flowers, nurseries, and orchards. The largest urban areas are the cities of Santa Rosa, 

Petaluma, Rohnert Park, Windsor, and Napa.

Municipal water use accounts for nearly half of the total water use in the study unit; 

the remainder is used for irrigated agriculture. Groundwater accounts for about a quarter of 

the municipal supply, depending on the area, and surface water accounts for the remainder. 

Recharge to groundwater is primarily stream-channel infiltration from the major rivers and 

their tributaries, and infiltration of water from precipitation and irrigation. The primary 

sources of discharge are water pumped for irrigation and municipal supply, evaporation, 

and discharge to streams.

NAPA

COUNTY

SONOMA

COUNTY

SOLANO

COUNTY

MARIN

COUNTY

WILSON GROVE

FORMATION

HIGHLANDS 

VALLEYS

AND PLAINS

VOLCANIC

HIGHLANDS

PETALUMA

VALLEY 

SANTA ROSA VALLEY

NAPA-SONOMA VALLEY

ALEXANDER VALLEY

LOWER RUSSIAN

RIVER VALLEY 

KENWOOD

VALLEY 

Santa Rosa

Calistoga

Rohnert

Park

Petaluma

Napa

Sonoma

Windsor Lake Berryessa

0 5

0 5 10 Kilometers

10 Miles

N o r t h C o a s t R a n g e s

Sonoma Mts

M a y a c m a s M t s

H o w e l l M t s

Lake

Sonoma

San Pablo Bay

Pacific Ocean

Organic

constituents

Inorganic

constituents

High Moderate

CONSTITUENT CONCENTRATIONS

Low or not detected 

Inorganics 

Values are a percentage of the area of the primary aquifers

with concentrations in the three specified categories.

50 36

14

94

5 1
 e

RESULTS: Groundwater Quality in the North 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 North 

San Francisco Bay study unit, trace elements were present at high concentrations 

in about 14% of the primary aquifers. Arsenic, boron, and lead were the trace 

elements that most frequently occurred at high concentrations. Aluminum, antimony, and nickel also were detected at high concentrations, but in less than (<) 

1% of the primary aquifers. Fluoride is a minor element that was present at high 

concentrations in about 1% of the primary aquifers and at moderate concentrations in <1%.

Radioactivity is the release of energy or energetic particles during structural 

changes in the nucleus of an atom. Most of the radioactivity in groundwater 

comes from decay of naturally occurring isotopes of uranium and thorium in 

minerals in the sediments of the aquifer. Radioactivity from the radioactive constituents occurred at low levels in 100% of the primary aquifers.

Nutrients, such as nitrate and nitrite, are 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. Nitrate was present at high concentrations in <1% 

of the primary aquifers, and nitrate was present at moderate concentrations in 

about 3% of the primary aquifers.

Inorganic Constituents with Non-Health Benchmarks

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

Some constituents, such as total dissolved solids (TDS) and chloride, affect 

the aesthetic properties of water, such as taste, color, and odor. Other constituents, such as iron and manganese, can create nuisance problems, such as scaling 

and staining.

The State of California has a recommended and an upper limit for TDS in 

drinking water. In the North San Francisco Bay study unit, TDS was present at 

high concentrations (greater than the upper limit) in about 1% of the primary 

aquifers. About 7% of the primary aquifers had moderate TDS concentrations 

(between the recommended and upper limit), and about 92% had low concentrations (less than the recommended limit).

Iron and manganese are naturally occurring elements, and either were present at high concentrations in about 42% of the primary aquifers. Iron or manganese were present at moderate concentrations in about 18% of the primary 

aquifers and at low concentrations in about 40%.

Perchlorate and N-Nitrosodimethylamine (NDMA)

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

Perchlorate, an inorganic constituent, and NDMA, a semi-volatile organic 

chemical, are of special interest in California because these constituents have 

recently been found in or are considered to have the potential to affect drinkingwater supplies. Their presence in groundwater is monitored by the California 

Department of Public Health (http://www.cdph.ca.gov). In the North San Francisco Bay study unit, perchlorate and NDMA were not detected in the primary 

aquifers. 

Trace and 

minor elements

Total 

dissolved 

solids

Nutrients

Radioactive

constituents

Iron or 

manganese

Perchlorate

and NDMA

INORGANIC CONSTITUENTS

SPECIAL INTEREST CONSTITUENTS

53

14

33

3<1

7

97

100

92

18

100

40 42

1
Organic Constituents

The Priority Basin Project uses laboratory methods that can detect low 

concentrations of volatile organic compounds (VOC) and pesticides, far below 

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

concentrations can be used to help trace water 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 into the air. 

Solvents are used for a number of purposes, including manufacturing and 

cleaning. In the North San Francisco Bay study unit, solvents were present at 

high concentrations in about 1% of the primary aquifers. The solvents found at 

high concentrations were tetrachloroethene and trichloroethene. Solvents were 

present at moderate concentrations in about 3% of the primary aquifers and 

were low in about 96%. Trihalomethanes may form during municipal water 

purification and enter groundwater by the infiltration of landscape irrigation 

water. Trihalomethanes were detected at low concentrations in the primary 

aquifers. 

Other VOCs include organic synthesis reagents and gasoline additives. 

Other VOCs were present at high concentrations in <1% of the primary aquifers, at moderate concentrations in about 1% of the primary aquifers, and at 

low concentrations in about 99%. The reagent found at high concentrations 

was 1,1-dichloroethene.

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 North San Francisco Bay study unit, insecticides were not 

detected at high concentrations in the primary aquifers, but the insecticide 

diazinon was detected at moderate concentrations in about 1% of the primary 

aquifers. Herbicides and fumigants were detected at low concentrations.

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) are used when available. Otherwise, nonregulatory benchmarks for protecting aesthetic properties, such as 

taste and odor (Secondary Maximum Contaminant Level, SMCL), and nonregulatory 

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

Advisory, HAL) are used.

Solvents

Trihalomethanes

Insecticides 

Other volatile

organic

compounds 

ORGANIC CONSTITUENTS

3

1

1

1

96

99

100

Herbicides and

fumigants

100

99

<1

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 are generally less prevalent and 

have smaller concentrations relative to benchmarks than inorganic constituents. Low concentrations include non-detections and values 

less than moderate concentrations. Methods for evaluating water quality are discussed by Kulongoski and others (2010).

High concentrations

Moderate concentrations

Low concentrations

EXAMPLE

Values are a percentage of the area of the primary aquifers

with concentrations in the three specified categories.

CONSTITUENT CONCENTRATIONS

[ < , less than]

RESULTS: Groundwater Quality in the North San Francisco Bay Study Unit
Factors that Affect Groundwater Quality

In the North San Francisco Bay study unit, arsenic is the constituent that most 

frequently exists at high concentrations in the primary aquifers (about 10%). Natural 

sources of arsenic include the dissolution of arsenic-rich minerals such as apatite and 

arsenian pyrite, a common constituent of shale. Arsenic has been used as a wood preservative, in glass production, and in the mining of copper and gold, and consequently 

might enter groundwater as a result of these uses. The human-health regulatory benchmark for arsenic is 10 micrograms per liter.

In the North 

San Francisco Bay 

study unit, nearly 

all of the samples 

having high arsenic concentrations 

were collected 

from wells in the 

Valleys and Plains 

study area. The 

wells with groundwater containing high arsenic 

concentrations are 

grouped into four 

areas: the Santa 

Rosa Valley, the 

southern Napa 

Valley, the Calistoga area, and 

the Agua Caliente 

area.

The elevated 

arsenic concentrations in groundwaters from the Santa Rosa Valley and southern Napa Valley are primarily caused by 

the release of arsenic during dissolution of iron or manganese oxides under iron- or 

manganese-reducing (anoxic) conditions (Kulongoski and others, 2010).

The elevated arsenic concentrations in the Calistoga and Agua Caliente hydrothermal areas most likely result from shallow groundwater mixing with deep thermal 

waters, which have elevated temperatures and high pH values. The increase in arsenic 

solubility with increase in water temperature, and the desorption or inhibition of sorption 

of arsenic to aquifer sediments under alkaline conditions (pH greater than 8.0) (Ballantyne and Moore, 1988; Welch and others, 2000) likely contribute to the higher arsenic 

concentrations in groundwater from the Calistoga and Agua Caliente hydrothermal 

areas.

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 shallower and 

deeper parts may differ from that in the 

primary aquifers. GAMA’s Domestic 

Well Project assesses water quality 

in the shallower parts of the aquifer 

system. 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 waterquality, hydrologic, geographic, and 

other data to help assess the factors that 

affect water quality. In the North San 

Francisco Bay study unit, data were 

collected by the PBP in 2004 and from 

the CDPH database for 2001–2004. 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.

Lake Berryessa

0 5

0 5 10 Kilometers

10 Miles

Lake

Sonoma

San Pablo Bay

Pacific Ocean

WILSON GROVE

FORMATION

HIGHLANDS 

VALLEYS

AND PLAINS

VOLCANIC

HIGHLANDS

CDPH well USGS grid well

0-5

5.1-10

10.1-98

ARSENIC, IN MICROGRAMS PER LITER

0-5

5.1-10

10.1-33

Low

Moderate

High

Relative-concentration

Santa

Rosa

Valley

Southern

Napa

Valley

Calistoga

Agua

Caliente

By Justin T. Kulongoski and Kenneth Belitz

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

For more information

Technical reports and hydrologic data 

collected for the GAMA Program 

SELECTED REFERENCES may be obtained from

Ballantyne, J.M., and Moore, J.N., 1988, Arsenic geochemistry in geothermal systems: Geochimica et Cosmochimica Acta, v. 52, p. 475-483.

California Department of Water Resources, 2003, California’s groundwater: California Department of Water Resources Bulletin 118, 246 p. Available at http://www.groundwater.water.

ca.gov/bulletin118 .

Kulongoski, J.T., Belitz, Kenneth, and Dawson, B.J., 2006, Ground-water quality data in the 

North San Francisco Bay Hydrogeologic Provinces, California, 2004: Results from the California Ground-Water Ambient Monitoring and Assessment Program: U.S. Geological Survey 

Data Series Report 167, 100 p. Available at http://pubs.usgs.gov/ds/ds167 .

Kulongoski, J.T., Belitz, Kenneth, Landon, M.K., and Farrar, Christopher, 2010, Status and 

understanding of groundwater quality in the North San Francisco Bay Groundwater Basins, 

2004: California GAMA Priority Basin Project: U.S. Geological Survey Scientific Investigations Report 2010-5089, 87 p. Available at http://pubs.usgs.gov/sir/2010/5089/ .

Welch, A.H., Westjohn, D.B., Helsel, D.R., and Wanty, R.B., 2000, Arsenic in ground water of 

the United States—Occurrence and geochemistry: Ground Water, v. 38, no. 4, p. 589-604.