U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2018–5003

Version 1.1, February 2019

Prepared in cooperation with the East Bay Municipal Utility District, City of Hayward, and 

Alameda County Water District

Hydrogeologic Controls and Geochemical Indicators of 

Groundwater Movement in the Niles Cone and Southern 

East Bay Plain Groundwater Subbasins, Alameda County, 

California

Hydrogeologic Controls and Geochemical 

Indicators of Groundwater Movement in 

the Niles Cone and Southern East Bay Plain 

Groundwater Subbasins, Alameda County, 

California

By Nick Teague, John Izbicki, Jim Borchers, Justin Kulongoski, and 

Bryant Jurgens

Prepared in cooperation with the East Bay Municipal Utility District, City of 

Hayward, and Alameda County Water District

Scientific Investigations Report 2018–5003

Version 1.1, February 2019

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DAVID BERNHARDT, Acting Secretary

U.S. Geological Survey

William H. Werkheiser, Deputy Director 

exercising the authority of the Director

U.S. Geological Survey, Reston, Virginia: 2019 

First release: February 2018

Revised: February 2019 (ver. 1.1)

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Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials 

as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

Teague, Nick, Izbicki, John, Borchers, Jim, Kulongoski, Justin, and Jurgens, Bryant, 2018, Hydrogeologic controls 

and geochemical indicators of groundwater movement in the Niles Cone and southern East Bay Plain groundwater 

subbasins, Alameda County, California (ver 1.1, February 2019): U.S. Geological Survey Scientific Investigations 

Report 2018–5003, 62 p., https://doi.org/10.3133/sir20185003.

ISSN 2328-0328 (online)
iii

Contents

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................2

Purpose and Scope ..............................................................................................................................2

Description of the Study Area ............................................................................................................2

Hydrogeology................................................................................................................................4

The Upper Aquifer System ................................................................................................5

Deep Aquifer........................................................................................................................5

Recharge and Discharge...................................................................................................6

Groundwater Management........................................................................................................6

Methods...........................................................................................................................................................7

Groundwater-Level Measurement.....................................................................................................7

InSAR Data Processing .......................................................................................................................8

Streamflow Gains and Losses Estimation ........................................................................................8

Water Sample Collection and Analysis...........................................................................................10

Collection and Analysis of Core and Cuttings Material................................................................10

Hydrogeology................................................................................................................................................11

Groundwater Movement ...................................................................................................................11

Local Short-Term Land-Surface Displacement .............................................................................11

Streamflow Gains and Losses in Alameda Creek .........................................................................15

Geochemistry................................................................................................................................................18

Chemistry of Groundwater................................................................................................................18

Physical Properties and Chemical Characteristics of Groundwater................................18

Major-Ion Composition .............................................................................................................21

Chloride-to-Iodide Ratios .........................................................................................................21

Geochemical Indicators of Groundwater Movement..........................................................23

Noble-Gas and Tritium Analysis .......................................................................................................23

Tritium and Helium.....................................................................................................................25

Tritium-Helium-3 Ages...............................................................................................................25

Helium-4 Ages ............................................................................................................................26

Isotopic Composition of Groundwater ............................................................................................27

Oxygen-18 and Deuterium........................................................................................................27

Carbon-14 and Carbon-13.........................................................................................................29

Interpretation of Carbon-14 Data ...................................................................................30

Limitations of Carbon-14 Interpretations ......................................................................33

Summary........................................................................................................................................................34

References Cited..........................................................................................................................................35

Appendix 1. Location and Construction Data and Water-Level Measurements Collected by the 

U.S. Geological Survey During 2002 for Wells Drilled in the Niles Cone and Southern East 

Bay Plain Groundwater Subbasins .............................................................................................41

Appendix 2. U.S. Geological Survey National Water-Quality Laboratory Analytical Methods 

and Reporting Levels for Analysis of Groundwater and Surface-Water Samples..............45

References Cited.................................................................................................................................45
iv

Appendix 3. Aquifer Mineralogy, Niles Cone Groundwater Subbasin, Alameda County, 

California..........................................................................................................................................47

References Cited.................................................................................................................................47

Appendix 4. Streamflow Data Collected by the U.S. Geological Survey during April 2002..........51

Appendix 5. Physical Property, Major-Ion, Trace-Element, and Isotopic Data for Groundwater, 

Stream-Water, and Precipitation Samples Collected and Analyzed by the U.S. Geological 

Survey...............................................................................................................................................53

Appendix 6. Noble Gas and Tritium Data for Groundwater Samples Collected and Analyzed by 

the U.S. Geological Survey ...........................................................................................................59

Appendix 7. Measured and Interpreted Carbon-13 and Carbon-14 Data for Groundwater 

Samples Collected and Analyzed by the U.S. Geological Survey ..........................................61

Contents—Continued

Figures

1. Map showing location of the Niles Cone and southern East Bay Plain groundwater 

subbasins and municipal wells, including aquifer reclamation program wells, 

Alameda County, California.........................................................................................................3

2. Graph showing generalized A–A’ cross section showing groundwater aquifers of 

Niles Cone and southern East Bay Plain groundwater subbasins and well location 

and well construction for wells sampled as part of this study, Alameda County, 

California ........................................................................................................................................4

3. Map showing water-level elevation contours and water-level elevations in wells 

screened in the upper aquifer system, gaining and losing reaches along Alameda 

Creek, Quarry Lakes Regional Park recharge area, Alameda Creek, and Alameda 

County Water District aquifer reclamation program wells, Alameda County, 

California, April 2002.....................................................................................................................9

4. Map showing water-level elevation contours and water-level elevations in wells 

screened in the Deep aquifer; Quarry Lakes Regional Park recharge area; Alameda 

Creek; and Alameda County Water District Aquifer Reclamation Program wells, 

Niles Cone groundwater subbasin, Alameda County, California, 2002..............................12

5. Graphs showing precipitation at San Francisco International Airport, water-level 

elevation at infiltration pond Lago Los Osos, total pumpage from Alameda County 

Water District’s Aquifer Reclamation Program wells, and groundwater elevations in 

selected wells north from Alameda Creek in the Niles Cone groundwater subbasin, 

Alameda County, California.......................................................................................................13

6. InSAR interferogram displaying relative subsidence or uplift in the Niles Cone 

groundwater subbasin during refilling of infiltration ponds at Quarry Lakes 

Regional Park, Alameda County, California............................................................................14

7. Graphs showing streamflow and water-temperature measurements along 

Alameda Creek, April 24–25, 2002, Alameda County, California..........................................16

8. Cross-sectional bathymetry of Alameda Creek.....................................................................17

9. Boxplots showing pH, dissolved oxygen, and selected major-ion, nutrient, and 

trace-element concentrations in water from wells sampled in the Niles 

Cone and southern East Bay Plain groundwater subbasins, Alameda County, 

California, 2002–03......................................................................................................................19

10. Piper diagram showing major-ion composition of samples from selected wells in 

the Niles Cone and southern East Bay Plain groundwater subbasins, Alameda 

County, California, 2002–03........................................................................................................20
v

11. Chloride-to-iodide ratios as a function of chloride concentration in water 

from wells, Niles Cone and southern East Bay Plain groundwater subbasins, 

Alameda County, California, 2002–03.......................................................................................22

12. Graph showing selected noble-gas concentrations in water from selected wells 

in the Niles Cone and southern East Bay Plain groundwater subbasins, Alameda 

County, California, 2002–03........................................................................................................24

13. Graph showing spatial distribution of tritium concentrations in groundwater 

from selected Deep aquifer wells in the Niles cone and southern East Bay Plain 

groundwater subbasins, Alameda County, California, 2002–03..........................................26

14. Map showing spatial distribution of 4He ages from selected wells in the Niles 

Cone and southern East Bay Plain groundwater subbasins, Alameda County, 

California, 2002–03......................................................................................................................28

15. Graphs showing relations of delta oxgen-18 with delta deuterium (δD) in water from 

wells, Niles Cone and southern East Bay Plain groundwater subbasins, Alameda 

County, California, 2002–03........................................................................................................29

16. Graphs showing selected changes in chemical and isotopic composition of 

water from wells used to interpret carbon-14 data along section B–B’, Niles 

Cone and southern East Bay Plain groundwater subbasins, Alameda County, 

California, 2002–03......................................................................................................................31

17. Plot of rank order carbon-14 data, expressed as cumulative exceedance 

percentage, in water from sampled wells in the Niles Cone and southern East 

Bay Plain groundwater subbasins, Alameda County, California, 2002–03. Tritium 

concentrations are shown using filled and open circle symbols.......................................33

3–1. Scanning electron microscopy images of typical mineral grains from core material 

from selected sites in the Niles Cone groundwater subbasin, Alameda County, 

California ......................................................................................................................................47

Figures—Continued

Tables

1–1. Location and construction data and water-level measurements collected by the 

U.S. Geological Survey during fall 2002 for wells drilled in the Niles Cone and 

southern East Bay Plain groundwater subbasins, Alameda County, California ..............41

2–1. U.S. Geological Survey National Water-Quality Laboratory analytical methods and 

reporting levels for analysis of groundwater samples.........................................................46

3–1. Elemental composition of samples from Lake Chad well (4S/2W-14D3) at 517 feet 

deep and outcrop on northwest shore of Quarry Lakes, Niles Cone groundwater 

subbasin, Alameda County, California.....................................................................................48

3–2. Mineralogical composition and optical observations of samples from Lake Chad 

well (4S/2W-14D3) at 517 feet deep and outcrop on northwest shore of Quarry 

Lakes, Niles Cone groundwater subbasin, Alameda County, California ...........................49

4–1. Streamflow data collected by the U.S. Geological Survey during April 2002, 

Alameda Creek, California.........................................................................................................51

5–1. Physical property, major-ion, selected trace-element, and isotopic data for 

groundwater, stream-water, and precipitation samples collected and analyzed by 

the U.S. Geological Survey, southern East Bay Plain and Niles Cone groundwater 

subbasins, Alameda County, California, 2002–03 ..................................................................53

6–1. Noble gas and tritium data for groundwater samples collected from selected wells 

in the Niles Cone and southern East Bay Plain groundwater subbasins, Alameda 

County, California, March–October, 2002–03 .........................................................................59
vi

7–1. Measured and interpreted carbon-13 and carbon-14 data for groundwater samples 

collected from selected wells in the Niles Cone and southern East Bay Plain 

groundwater subbasins, Alameda County, California, March–October, 2002..................61

7–2. Chemical reactions used to interpret carbon-14 data .........................................................62

Tables—Continued

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

Length

inch (in.) 25.4 millimeter (mm)

inch (in.) 25,400 micrometer (μm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609

Area

acre 4,047 square meter (m2)

acre 0.004047 square kilometer (km2)

square foot (ft2) 0.0929 square meter (m2)

square foot (ft2) 0.0011 square centimeter (cm2)

square mile (mi2) 2.590 square kilometer (km2)

Volume

gallon (gal) 3.785 liter (L)

acre-foot (acre-ft) 1,233 cubic meter (m3)

acre-foot (acre-ft) 1.233×109 cubic centimeter (cm3)

acre-foot (acre-ft) 1.233×1012 micro-cubic centimeter (μcm3)

Flow rate

acre-foot per year (acre-ft/yr) 1,233 cubic meter per year (m3/yr)

foot per day (ft/d) 0.3048 meter per day (m/d)

foot per minute (ft/min) 0.3048 meter per minute (m/min)

foot per second (ft/s) 0.3048 meter per second (m/s)

gallon per day (gal/d) 0.003785 cubic meter per day (m3/d)

gallon per minute (gal/min) 0.003785 cubic meter per minute (m3/min)

Density

pound-mass per cubic foot (lbm/ft3) 0.0160 grams per cubic centimeter (g/cm3)

Mass

pound, avoirdupois (lb) 0.4536 kilogram (kg) 

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F = (1.8 × °C) + 32.

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as follows:

°C = (°F − 32) / 1.8.

Specific storage is reported in units of per foot (ft−1).
vii

Specific conductance is reported in units of microsiemens per centimeter at 25 degrees Celsius 

(μS/cm at 25 °C).

Concentrations of chemical constituents in water are reported either in units of milligrams per 

liter (mg/L) or micrograms per liter (μg/L).

Concentrations of chemical constituents in sediment (alluvium) are reported either in units of 

milligrams per kilogram (mg/kg) or micrograms per cubic centimeter (μg/cm3).

Concentrations of the noble gases helium (He), neon (Ne), and krypton (Kr) are reported in 

units of micro-cubic centimeters (at standard temperature and pressure) per kilogram of water 

(μcm3(STP)/kg).

Concentrations of the noble gas argon (Ar) are reported in units of cubic centimeters (at 

standard temperature and pressure) per kilogram of water (cm3(STP)/kg).

Deep crustal flux of helium-4 is reported in units of cubic centimeters (at standard temperature 

and pressure) per square centimeter per year (cm3(STP)cm−2yr−1).

Concentrations of excess air are reported in units of cubic centimeters (at standard temperature 

and pressure) per kilogram of water (cm3/kg).

Concentrations of uranium (U) and thorium (Th) are reported in units of milligrams per kilogram 

of alluvium (mg/kg, ppm).

Concentrations of tritium (3H) are reported in units of tritium units (TU). The conversion of 

tritium units (TU) to picocuries per liter, based upon a tritium half-life of 12.32 years (Lucas and 

Unterweger, 2000), is 1 TU = 3.22 picocuries per liter.

Helium-3 (3He) data are reported as δ values computed from the formula:

  



 



  



 



 R

R

X

STD

1 100

where Rx is the ratio of 3He to 4He in the sample, RSTD is the 3He to 4He ratio of the reference 

standard air (1.384×10−6), and δ3He is expressed in parts per hundred.

Stable isotopes of water are reported as δ values computed from the formula:

  



 



  



 



 R

R

X

STD

1 1,000

where Rx is the ratio of 2H to 1H or 18O to 16O in the sample, RSTD is the 2H to 1H or 18O to 16O ratio of the reference standard Vienna Standard Mean Ocean Water 

(VSMOW), and δ2H or δ18O is expressed in parts per thousand.

Stable isotopes of carbon are reported as δ values computed from the formula:

  



 



  



 



 R

R

X

STD

1 1,000

where Rx is the ratio of 13C to 12C in the sample, RSTD is the 13C to 12C ratio of the reference 

standard Vienna Peedee Belemnite, and δ13C is expressed in parts per 

thousand.
viii

Datum

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88), unless otherwise noted.

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Mean sea level is 6.75 feet above the station datum for station 9414750, Alameda, California, of 

3.56 feet (NAVD 88).

Abbreviations

Ao initial carbon activity

ACWD Alameda County Water District

ANOVA analysis of variance

Ar argon

ARP aquifer reclamation program

ASR aquifer storage and recovery

BGP Bayside Groundwater Project

°C degrees Celsius

14C carbon-14, in percent modern carbon

CE closed system equilibrium

cfs cubic feet per second

CO2 carbon dioxide; molecular formula

DIC dissolved organic carbon

DOD U.S. Department of Defense

EBMUD East Bay Municipal Utility District

EPA U.S. Environmental Protection Agency

GMWL Global Meteoric Water Line

H2O water; molecular formula

2

H deuterium

3

H tritium

He helium

3

He helium-3; isotope of helium

3

Hetrit tritiogenic helium-3

4

He helium-4; isotope of helium

4

Heex excess helium-4

InSAR interferometric synthetic aperture radar
ix

Kr krypton

kyr thousand years

MCL maximum contaminant level

Myr million years

NGT groundwater recharge temperature

Ne neon

ΔNe neon oversaturation

NWQL National Water Quality Laboratory

18O oxygen-18

pmC percent modern carbon

ppm parts per million

PR partial reequilibration

SFPUC San Francisco Public Utilities Commission

SI saturation indexes

SMCL secondary maximum contaminant level

STP standard temperature and pressure

SWP State Water Project

TU tritium unit

UA unfractionated air

USGS U.S. Geological Survey

VSMOW Vienna Standard Mean Ocean Water

ybp years before present

Abbreviations—Contiued
x
Hydrogeologic Controls and Geochemical Indicators of 

Groundwater Movement in the Niles Cone and Southern 

East Bay Plain Groundwater Subbasins, Alameda County, 

California

By Nick Teague, John Izbicki, Jim Borchers, Justin Kulongoski, and Bryant Jurgens

Abstract

Beginning in the 1970s, Alameda County Water District 

began infiltrating imported water through ponds in repurposed 

gravel quarries at the Quarry Lakes Regional Park, in the Niles 

Cone groundwater subbasin, to recharge groundwater and to 

minimize intrusion of saline, San Francisco Bay water into 

freshwater aquifers. Hydraulic connection between distinct 

aquifers underlying Quarry Lakes allows water to recharge the 

upper aquifer system to depths of 400 feet below land surface, 

and the Deep aquifer to depths of more than 650 feet. Previous 

studies of the Niles Cone and southern East Bay Plain 

groundwater subbasins suggested that these two subbasins 

may be hydraulically connected. Characterization of storage 

capacities and hydraulic properties of the complex aquifers 

and the structural and stratigraphic controls on groundwater 

movement aids in optimal storage and recovery of recharged 

water and provides information on the ability of aquifers 

shared by different water management agencies to fulfill 

competing storage and extraction demands. The movement of 

recharge water through the Niles Cone groundwater subbasin 

from Quarry Lakes and the possible hydraulic connection 

between the Niles Cone and the southern East Bay Plain 

groundwater subbasins were investigated using interferometric 

synthetic aperture radar (InSAR), water-chemistry, and 

isotopic data, including tritium/helium-3, helium-4, and 

carbon-14 age-dating techniques.

InSAR data collected during refilling of the Quarry 

Lakes recharge ponds show corresponding ground-surface 

displacement. Maximum uplift was about 0.8 inches, 

reasonable for elastic expansion of sedimentary materials 

experiencing an increase in hydraulic head that resulted from 

pond refilling. Sodium concentrations increase while calcium 

and magnesium concentrations in groundwater decrease along 

groundwater flowpaths from the Niles Cone groundwater 

subbasin through the Deep aquifer to the northwest toward 

the southern East Bay Plain groundwater subbasin. Residual 

effects of pre-1970s intrusion of saline water from San 

Francisco Bay, including high chloride concentrations in 

groundwater, are evident in parts of the Niles Cone subbasin. 

Noble gas recharge temperatures indicate two primary 

recharge sources (Quarry Lakes and Alameda Creek) in the 

Niles Cone groundwater subbasin. Although recharge at 

Quarry Lakes affects hydraulic heads as far as the transition 

zone between the Niles Cone and East Bay Plain groundwater 

subbasins (about 5 miles), the effect of recharged water on 

water quality is only apparent in wells near (less than 2 miles) 

recharge sources. Groundwater chemistry from upper aquifer 

system wells near Quarry Lakes showed an evaporated signal 

(less negative oxygen and hydrogen isotopic values) relative 

to surrounding groundwater and a tritium concentration 

(2 tritium units) consistent with recently recharged water from 

a surface-water impoundment. 

Uncorrected carbon-14 activities measured in water 

sampled from wells in the Niles Cone groundwater subbasin 

range from 16 to 100 percent modern carbon (pmC). The 

geochemical reaction modeling software NETPATH was used 

to interpret carbon-14 ages along a flowpath from Quarry 

Lakes toward the East Bay Plain groundwater subbasin. 

Model results indicate that changes in groundwater chemistry 

are controlled by cation exchange on clay minerals and 

weathering of primary silicate minerals. Old groundwater 

(lower carbon-14 activities) is characterized by high 

dissolved silica and pH. Interpreted carbon-14 ages ranged 

from 830 to more than 7,000 years before present and are 

less than helium-4 ages that range from 2,000 to greater 

than 11,000 years before present. The average horizontal 

groundwater velocity along the studied flowpath, as calculated 

using interpreted carbon-14 ages, through the Deep aquifer 

of the Niles Cone groundwater subbasin is between 3 and 

12 feet per year. The groundwater velocity decreases near 

the boundary of the transition zone to the southern East Bay 

Plain groundwater subbasin to about 0.5 feet per year. These 

changes may result from water recharged from different 

sources converging in flowpaths north of the transition zone, 

or a boundary to flow between the Niles Cone and southern 

East Bay Plain groundwater subbasins, likely owing to 

changes in lithology caused by depositional patterns.
2 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Introduction

Water agencies in the east San Francisco Bay area are 

developing alternate water supplies to supplement current 

sources largely imported from reservoirs in the Sierra Nevada 

or the Sacramento–San Joaquin River Delta. Conjunctive-use 

practices utilizing artificial storage and recovery of surface 

water in aquifers are being implemented as means to address 

water-supply issues related to the growing demand for 

municipal and industrial water and the temporal variability of 

the surface-water supply. In addition, increased development 

of local groundwater through managed aquifer recharge has 

been proposed as an alternative to imported water as a means 

to address the potential interruption of aqueduct flows during 

seismic or other emergencies (Alameda County Water District, 

2001b). 

The study area, the Niles Cone and southern East Bay 

Plain groundwater subbasins, is in the alluvial plain south of 

Oakland, California, on the eastern shore of the south San 

Francisco Bay (fig. 1). The area is underlain by a complex 

aquifer system at least 650 feet (ft) thick (fig. 2). Several water 

management projects are being developed as alternate and 

emergency water sources in the area. The Alameda County 

Water District (ACWD) recharges aquifers by infiltrating 

surface water from local reservoirs and from the South Bay 

Aqueduct (not shown on figures) through abandoned gravel 

quarries at Quarry Lakes Regional Park and at impoundments 

behind inflatable rubber dams in the channel of Alameda 

Creek (Alameda County Water District, 2001a). The City of 

Hayward has constructed five deep water-supply wells in the 

aquifers underlying Hayward, Calif., to provide emergency 

water supply. The East Bay Municipal Utility District 

(EBMUD) has tested the feasibility of artificial storage and 

recovery (ASR) of water through deep wells near the San 

Francisco Bay (Bayside), just south from San Lorenzo Creek 

(fig. 1; Luhdorff and Scalmanini Consulting Engineers, 2003). 

Conjunctive-use programs store a combination of surface 

water and groundwater, and therefore, they require aquifer 

systems capable of storing and subsequently yielding large 

quantities of water (Mariño, 2001). The ability of aquifers 

shared by different water management agencies to fulfill 

competing storage and extraction demands may be difficult 

to evaluate in the absence of regional hydrogeology data. 

Characterization of storage capacities and hydraulic properties 

of the complex aquifers and the structural and stratigraphic 

controls on groundwater movement aids in optimal storage 

and recovery of recharged water. 

Local water agency staff, their consultants and 

representatives, and the U.S. Geological Survey (USGS) are 

collaborating to develop an understanding of hydrogeologic 

factors that affect groundwater development and successful 

operation of conjunctive-use facilities in the study area. 

Previously, the USGS, in cooperation with EBMUD, 

investigated the hydrogeology and geochemistry of aquifers 

underlying the southern East Bay Plain groundwater subbasin 

(Izbicki and others, 2003; Sneed and others, 2015). They 

found that (1) most recent recharge to the aquifer system 

is restricted to shallow aquifers near the mountain front; 

(2) recharge occurs as infiltration of streamflow during the 

winter and as infiltration from more diffuse sources such as 

precipitation, irrigation, and septic discharge; and (3) large 

amounts of recharge from imported water leaking from water 

supply pipes is not apparent. This report extends that work 

further south, describing the results of an investigation of parts 

of the Deep aquifer underlying the southern East Bay Plain 

and the northern Niles Cone groundwater subbasins that was 

completed cooperatively with ACWD, City of Hayward, and 

EBMUD.

Purpose and Scope

Given increasing demands on groundwater resources 

and often competing groundwater management projects in 

aquifers underlying the Niles Cone and southern East Bay 

Plain groundwater subbasins, local management agencies 

require improved understanding of the movement of recharged 

water within and between aquifers and the potential effect of 

groundwater recharge projects in urban areas. The purpose 

of this report is to document the methods and results of 

an evaluation of the geologic and hydrologic controls on 

groundwater movement through aquifers between the Niles 

Cone and southern East Bay Plain groundwater subbasins on 

the east side of San Francisco Bay, California.

The scope of this report includes the methods for 

collection of hydrologic, InSAR, and geochemical data for 

2002 and 2003; the description of the analysis of the data to 

evaluate movement of water from the Quarry Lakes Regional 

Park recharge ponds and Alameda Creek into the aquifer 

system of the Niles Cone groundwater subbasin; and the 

interaction of groundwater in the Niles Cone and southern 

East Bay Plain groundwater subbasins.

Description of the Study Area

The study area is composed of the alluvial fans (locally 

referred to as cones) of the San Lorenzo and Alameda Creeks 

and smaller tributaries, and it is separated into two distinct 

groundwater subbasins: the East Bay Plain groundwater 

subbasin and the Niles Cone groundwater subbasin. The East 

Bay Plain groundwater subbasin is about 120 square miles 

of tidal marshes and alluvial lowlands near Oakland, Calif., 

on the east side of San Francisco Bay (fig. 1). The Niles 

Cone groundwater subbasin is formed by the alluvial plain 

of Alameda Creek and is 103 square miles. The area has a 

Mediterranean climate with mild, wet winters and warm, dry 

summers. The average annual temperature is 15 °C and ranges 

from 11 °C (December–February) to 18 °C (June–September; 

National Oceanic and Atmospheric Administration, 2012). 

Most precipitation falls as rain between November and March 

and averages 23 inches (in.) annually (Muir, 1997). The area 

is highly urbanized with diverse residential, commercial, and 

industrial land uses. Although agriculture was important in the 

past, there is little agricultural land use in the study area at the 

present time.
Introduction 3

Sac15-0557_fig 01

MISSION FAULT

HAYWARD FAULT

SILVER CREEK FAULT

0 5 10 MILES

0 5 10 KILOMETERS

17M7,

17M8,

17M6

13P4, 13P6,

12K10,

12K8

12C1

10E4

4R1 3L1

4E1 4F3 2H1

15L5

14D3, 14D4

 13P7, 13P5

20L20 Well A

Mowry well field

29L6

ARP wells

19Q3

Bayside DIABLO RANGE

122°20' 122°15' 122°10' 122°05' 122°00' 121°55'

37°

45'

37°

40'

37°

35'

37°

30'

A

A’

Leandro synform

Old Alameda

Creek

Dry

Creek

Quarry Lakes

Regional Park Alameda Creek

Coyote Hills

B

B’

Study area

Sacramento–

San Joaquin

River Delta

Hetch Hetchy

Reservoir SIERRA NEVADA RANGE

Yosemite

National

Park

Fremont

Oakland

San Lorenzo

Hayward

San Leandro

San Francisco

Bay

San Leandro Creek San Leandro Creek

San Lorenzo CreekSan Lorenzo Creek

EXPLANATION

12K10

13P5

19Q3

Well A

A A’

Municipal wells

Wells sampled by Izbicki and others, 2003

Wells sampled as part of this study

 Upper aquifer system wells

 Deep aquifer wells

Surface water site

Transition zone (Luhdorff and Scalmanini

 Consulting Engineers, 2003)

East Bay Plain subbasin

Niles Cone subbasin

Line of hydrogeologic section

make sure this is in figure caption ‘aquifer reclamation program (ARP) ’

San Francisco

International Airport

Dry

Creek

Background image is the intellectual property of Esri and is used herein under license.

Copyright © 2014 Esri and its licensors. All rights reserved. Base modified from U.S.

Geological Survey digital data, various scales; Lambert Conformal Conic projection;

North American Datum of 1983

Figure 1. Location of the Niles Cone and southern East Bay Plain groundwater subbasins and municipal wells, including aquifer 

reclamation program (ARP) wells, Alameda County, California.
4 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Hydrogeology

The study area is located where the right-lateral San 

Andreas Fault splays into a number of active subparallel 

right-lateral fault zones, including the Hayward Fault (fig. 1). 

The San Francisco Bay, surrounding marshes, and alluvial 

plains lie in a depression in the San Francisco Bay block, 

a structural province between the Diablo Range and the 

Hayward fault zone to the east and the Santa Cruz Mountains 

and San Andreas Fault to the west (not shown on figures). East 

from the Hayward Fault, Tertiary volcanic and sedimentary 

rocks; pre-Tertiary, unmetamorphosed rocks of the Great 

Valley sequence; and rocks of the Franciscan complex crop 

out in the Diablo Range (Wallace, 1990; Graymer and others, 

1995; Graymer, 2000; Graymer, 2003). Within the structural 

depression, sedimentary deposits of variable thickness overlie 

the buried erosional surface of consolidated Franciscan 

Complex bedrock (Rogers and Figuers, 1991). The underlying 

Franciscan bedrock is of limited importance for water supply 

(Fugro West Inc., 2000, 2001; Dave Thomas, California 

Department of Transportation, written commun., 2002). Where 

water is present within these deposits, it is more mineralized 

and less desirable for human consumption than fresher 

groundwater in the overlying alluvium. The thickness, extent, 

structure, and texture of the alluvial aquifer systems have 

been influenced by tectonic movement in the Hayward fault 

zone, paleoclimate and sea level changes, and differences in 

sediment source areas.

SAC15-0557_fig 02

2H1

Deep aquifer

southern East Bay Plain

upper aquifers (undifferentiated)

Deep aquifer

EXPLANATION

Groundwater aquifer boundary

Groundwater aquifer boundary, inferred

Well

Abbreviated well number

Perforated interval and abbreviated well number

 (colors indicate perforated interval and well 

 number for a well in a well cluster)

Total depth

17M6

13P6

13P7

13P4

13P5

17M7

17M8

12K8

12K9

12K10

12K11

14D3

14D4

14D5

14D6

14D7 Upper

aquifer

system

NORTHWEST SOUTHEAST

Generalized cross section

SOUTHERN EAST BAY PLAIN

Elevation, in feet

OLD ALAMEDA CREEK ALAMEDA CREEK

29L6 10E4 14D 15L5 12K 13P

12C1 3L1

3L1

4F3

4R1

4E1 17M

TRANSITION ZONE NILES CONE

200

−200

−400

−600

−800

−1,000

−1,200

0

70,000 65,000 60,000 55,000 50,000 45,000 40,000 35,000 30,000 25,000 20,000 15,000 10,000 5,000 0

0

FEET

Fremont aquifer

Centerville aquifer

A A’

Modified from Luhdorff and Scalmanini

Consulting Engineers (2003)

Scale, in feet

Newark aquifer

20L20

Figure 2. Generalized A–A’ cross section showing groundwater aquifers of Niles Cone and southern East Bay Plain groundwater 

subbasins and well location and well construction for wells sampled as part of this study, Alameda County, California.
Introduction 5

The principal water-bearing units in the Niles Cone 

and southern East Bay Plain groundwater subbasins are 

located west of the Hayward Fault, which acts as an effective 

groundwater boundary (Clark, 1915). Four primary aquifers 

composed of Quaternary sedimentary deposits underlie 

the Niles Cone groundwater subbasin and southern East 

Bay Plain groundwater subbasins (California Department 

of Water Resources, 2003). The California Department of 

Water Resources (2003) delineated the subbasin boundaries 

by considering the geomorphic expression of present day 

alluvial fans, location of groundwater divides, political 

boundaries, and other factors. The aquifers (from shallowest 

to deepest) are the Newark, Centerville, Fremont, and Deep 

aquifers (fig. 2). The aquifers were first defined in the Niles 

Cone groundwater subbasin (California Department of Water 

Resources, 1967) and projected to the southern East Bay 

Plain groundwater subbasin by Brown and Caldwell (1986), 

Maslonkowski (1988), and Figuers (1998). Collectively, the 

aquifers consist of alluvial sand and gravel deposited by flood 

flows in Alameda Creek, presumably during glacial periods 

about 20,000, 120,000, and 240,000 years ago (Maslonkowski, 

1988; Koltermann and Gorelick, 1992), and are separated by 

estuarine mud or fine-grained alluvial flood-plain deposits. 

The Newark, Centerville, and Fremont aquifers are thicker 

and more continuous in the Niles Cone groundwater subbasin 

than in the East Bay Plain groundwater subbasin to the north 

(Luhdorff and Scalmanini Consulting Engineers, 2003). 

The Upper Aquifer System

In the Niles Cone groundwater subbasin, the Newark 

aquifer crops out at land surface, near the apex of the Alameda 

Creek alluvial fan, where it is 140 ft thick and lies 140 ft 

below land surface on the western edge of the area, where 

it thins to about 20 ft thick (California Department of Water 

Resources, 1967, 1968). Groundwater in the Newark aquifer 

is confined except near recharge areas along the mountain 

front (California Department of Water Resources, 2003). 

The Centerville aquifer lies at an average depth of 180 to 

200 ft below land surface and, similar to the Newark aquifer, 

thins to the west (California Department of Water Resources, 

2003). The Fremont aquifer lies between 300 and 390 ft 

below land surface, also thinning to the west. Groundwater in 

the Centerville and Fremont aquifers is confined (California 

Department of Water Resources, 2003). In parts of the Niles 

Cone groundwater subbasin where clay-rich aquitards are 

absent or thin, the Centerville and Fremont aquifers are 

hydraulically connected (Alameda County Water District, 

2001a). Given the Centerville and Fremont aquifers are 

adjacent and hydraulically connected to each other, they are 

often referred to as a single aquifer unit, the CentervilleFremont aquifer. 

Near the apex of the Niles Cone groundwater subbasin, 

the Hayward Fault hydraulically partitions the alluvial 

deposits (Clark, 1915), and Alameda County Water District 

(2001) manages groundwater upgradient and downgradient 

from the Hayward Fault as separate aquifer systems. 

Lithologic data from wells and aquifer-test data indicate that 

the Newark and Centerville aquifers extend westward under 

and beyond San Francisco Bay (California Department of 

Water Resources, 1967). Lithologic data also indicate that 

the aquifers of the Niles Cone groundwater subbasin thin and 

become finer grained to the southwest, eventually disappearing 

in a clay-rich zone in northern Santa Clara Valley (California 

Department of Water Resources, 1967). For the purpose of 

this study, the Newark, Centerville, and Fremont aquifers are 

collectively referred to as the upper aquifer system.

Unlike the Niles Cone groundwater subbasin to the south, 

alluvial fans in the southern East Bay Plain groundwater 

subbasin were deposited by lower energy streams. It is 

difficult to correlate sand and gravel layers over great 

distances between wells in the southern East Bay Plain 

groundwater subbasin (Muir, 1993). Fine-grained sediments 

deposited between alluvial fans interrupt lateral continuity of 

coarse-grained layers and inhibit interfan flow of groundwater. 

The Hayward Fault forms the eastern boundary of aquifers in 

the southern East Bay Plain groundwater subbasin. Alluvial 

deposits in the area east of the Hayward Fault are thin and 

contain insubstantial amounts of groundwater. 

The degree of hydraulic connection between the three 

shallow aquifers in the Niles Cone groundwater subbasin and 

their time-equivalent units in the southern East Bay Plain 

groundwater subbasin is not well defined, although aquifer 

sediments in the two areas may become more hydraulically 

connected with depth (Figuers, 1998). For example, the 

Fremont aquifer in the Niles Cone groundwater subbasin 

may be connected hydraulically to the Fremont aquifer in the 

southernmost East Bay Plain groundwater subbasin because 

both are thought to be composed of sediment deposited in 

the alluvial fan of Alameda Creek. Fremont-age sediment has 

been translated about 1.5 miles to the northwest from the Niles 

Cone groundwater subbasin into the southern East Bay Plain 

groundwater subbasin by right-lateral motion on the Hayward 

Fault (assuming an average geologic rate of movement of 30 ft 

per thousand years; Maslonkowski, 1988; Koltermann and 

Gorelick, 1992).

Deep Aquifer

Permeable sand and gravel layers that underlie the three 

shallowest aquifers (the upper aquifer system) in the study 

area are termed the Deep aquifer. Because relatively few wells 

have been drilled into the Deep aquifer, the thickness, areal 

extent, sedimentology and structure of the Deep aquifer is less 

well described than for the upper aquifer system. Permeable 

sand and gravel beds within the Deep aquifer are shallowest in 

the Niles Cone groundwater subbasin and deepen to the north, 

where they lie between 500 and 650 ft below land surface 

(fig. 2). In some areas, the aquifer can be as much as 150 ft 

thick.
6 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Thickness of the Deep aquifer does not decrease near 

the edge of the Niles Cone groundwater subbasin. In fact, the 

Deep aquifer is thickest and most continuous south of San 

Leandro, Calif. (Maslonkowski, 1988), and eventually thins, 

nearly disappearing to the north of the study area (not shown 

on fig. 2; CH2M-Hill, Inc., 2000). It is likely that the source 

of sediments in the Deep aquifer beneath San Lorenzo Creek 

alluvial fan, and perhaps even further north, is the Alameda 

Creek watershed and that tectonic activity has shifted the 

sediments to the north (Koltermann and Gorelick, 1992).

Recharge and Discharge

Under predevelopment (before the late 1850s) conditions, 

recharge to the aquifer systems occurred primarily as 

infiltration of streamflow from San Leandro, San Lorenzo, 

and Alameda Creeks. Smaller amounts of recharge are 

believed to have occurred as infiltration of precipitation. 

Muir (1996a) estimated that annual recharge from infiltration 

of streamflow and direct infiltration of precipitation in the 

East Bay Plain groundwater subbasin was about 3,500 

and 800 acre-feet (acre-ft), respectively. In the Niles Cone 

groundwater subbasin, recharge from infiltration of streamflow 

was about 14,000 acre-feet per year (acre-ft/yr; Bailey, 1919; 

California Department of Water Resources, 1968). Bailey 

(1919) regarded recharge from infiltrating precipitation in 

the Niles Cone groundwater subbasin as insignificant, but 

California Department of Water Resources (1968) estimated 

such recharge at about 7,400 acre-ft/yr. As noted earlier, some 

inflow to the Deep aquifer in the southern East Bay Plain 

groundwater subbasin may have occurred as groundwater that 

flowed northward from the Deep aquifer in the Niles Cone 

groundwater subbasin. 

The Hayward Fault is a barrier to groundwater flow 

between sedimentary deposits east and west of the fault. 

Under predevelopment conditions, groundwater discharging 

along the fault from sediments to the east maintained flow of 

springs (Figuers, 1998) that discharged groundwater at a rate 

of about 5,000 acre-ft/yr to extensive willow marshes north 

of San Lorenzo Creek and to other locations (Grossinger and 

Brewster, 2003). West of the Hayward Fault, groundwater 

flowed toward San Francisco Bay, where it discharged to tidal 

wetlands or continued to flow west under San Francisco Bay 

(Muir, 1996b). Where westward flow of groundwater was 

impeded by Franciscan Formation rocks in the subsurface 

near the Coyote Hills, groundwater discharged to wetlands or 

was diverted north and south from the Coyote Hills (Figuers, 

1998).

As a result of agricultural and urban development 

beginning in the late 1800s, groundwater pumping became 

an important discharge mechanism in the study area. More 

than 15,000 wells were drilled in the southern East Bay Plain 

groundwater subbasin between 1886 and 1950 (Figuers, 

1998). Most of these wells were less than 100 ft deep, 

although some wells were more than 400 ft deep, and a few 

were drilled to depths greater than 1,000 ft. About 250 wells 

within the ACWD service area are more than 400 ft deep 

(James Ingle, ACWD, written commun., 2004). In 1917, 

1,450 wells withdrew 19,000 acre-ft from the aquifers of the 

Niles Cone groundwater subbasin (Bailey, 1919). In 1960, 

1,042 wells withdrew about 46,500 acre-ft from wells in the 

aquifers of the Niles Cone groundwater subbasin (California 

Department of Water Resources, 1960). In 1990, estimated 

withdrawal was 32,000 acre-ft from the aquifers of the 

Niles Cone groundwater subbasin (Fio and Leighton, 1995). 

Groundwater pumping in excess of recharge caused water 

levels to decline to more than 100 ft below sea level during 

the mid-1920s, mid-1930s, and late 1940s (Figuers, 1998). 

Salty water from San Francisco Bay, or salt water evaporation 

ponds at the margin of San Francisco Bay, migrated inland 

through shallow aquifers to areas where sediments generally 

are coarser grained and more permeable than shoreward 

sediments. The California Department of Water Resources 

(1960) attributed increasing chloride concentrations in the 

Niles Cone groundwater subbasin to vertical flow from 

overlying intruded aquifers through permeable sediments in 

recharge areas near the mountain front, through gaps in clayey 

aquicludes, and through leaking and abandoned wells. 

Muir (1996a) estimated that recharge from leaky 

underground water-supply and sewer pipes was about 

3,100 acre-ft/yr in the southern East Bay Plain groundwater 

subbasin. However, Izbicki and others (2003), using 

stable isotope data from groundwater samples, suggested 

that recharge from leaking pipes may be less important 

than reported by Muir (1996a) or may not be uniformly 

distributed across the southern East Bay Plain groundwater 

subbasin. Natural recharge may have decreased as a result of 

urbanization because streams were channelized and lined with 

concrete, and permeable soil surfaces were paved.

Groundwater Management

In the mid-1900s, water imported to the study area 

reduced the dependence on local groundwater for public 

supply (California Department of Water Resources, 1963). The 

EBMUD imported surface water from the Sierra Nevada and 

also collected surface water in reservoirs in the hills east of 

the study area. The City of Hayward contracted with the San 

Francisco Public Utilities Commission (SFPUC) to purchase 

water for public supply from Hetch Hetchy Reservoir in 

northern Yosemite National Park. The ACWD also contracted 

with the SFPUC to purchase water from the Hetch Hetchy 

Reservoir and with the State Water Project to import water 

originating in the Sierra Nevada through the South Bay 

Aqueduct from the Sacramento–San Joaquin River Delta 

(Alameda County Water District, 2001a). The SFPUC and 

ACWD also collected runoff in local reservoirs. As the area 

became increasingly urbanized, agricultural pumping declined, 

and recharge from infiltration of imported water used for 

landscape irrigation increased. Groundwater levels recovered 

to near predevelopment conditions owing to the decreased 

dependence on local groundwater supplies (California 

Department of Water Resources, 1963).
Methods 7

Managed aquifer recharge in the Niles Cone groundwater 

subbasin includes water infiltrated at the Quarry Lakes 

Regional Park and behind two rubber dams that are inflated 

seasonally to impound water in Alameda Creek. The Quarry 

Lakes are a series of abandoned gravel quarries that were 

graded and plumbed to allow ACWD to operate them as 

artificial groundwater recharge facilities (fig. 1). The sources 

of water to Quarry Lakes are runoff in the Alameda Creek 

watershed, State Water Project (SWP) water imported since 

1962 from central California (primarily snowmelt from 

the Sierra Nevada), and water discharged from reservoirs 

in the Alameda Creek watershed, which contain both local 

runoff and SWP water. Part of the flow of Alameda Creek is 

groundwater pumped from gravel quarries in upstream parts 

of the watershed (Moran and Halliwell, 2004). During drought 

years prior to importation of SWP water, or later when SWP 

water was not available for flow augmentation in Alameda 

Creek, effluent discharged from wastewater treatment plants 

was a substantial component of streamflow (Lopp, 1981). 

In conjunction with managed aquifer recharge, ACWD’s 

Aquifer Reclamation Program (ARP) wells (fig. 1), which 

extract stratigraphically-trapped salty water, has substantially 

decreased the area of the Niles Cone groundwater subbasin 

affected by salt-water intrusion. The ACWD adds about 

30,000 acre-ft/yr to groundwater storage at Quarry Lakes and 

the rubber dam impoundments, and ACWD usually extracts 

less than 10,000 acre-ft/yr from ARP wells. The ACWD 

estimated that pumping of local groundwater for public and 

private supplies in the Niles Cone groundwater subbasin 

averaged about 24,000 acre-ft/yr during 1997–99 (Moran and 

Halliwell, 2004). 

An interferometric synthetic aperture radar (InSAR) 

interferogram (change from July 3, 1999, to January 29, 2000) 

indicated that land surface near ACWD’s managed aquifer 

recharge facilities and along Alameda Creek to the west is 

displaced upward as much as 0.8 in. (20 millimeters, mm) 

relative to areas northwest and southwest of the facilities. 

Land surface displacements related to rising groundwater 

levels in recharge areas has been demonstrated in other areas 

of California (Galloway and others, 1999; Lu and Danskin, 

2001; Bawden and others, 2001). These displacements may be 

a cause for concern in urban areas or may indicate potential 

for permanent (inelastic) subsidence of aquifer deposits should 

groundwater pumping lower water levels beyond previous 

levels (Galloway and others, 1999). 

In addition to managed aquifer recharge projects operated 

by ACWD, the City of Hayward has constructed five deep 

water-supply wells in the aquifers underlying Hayward, 

Calif., to provide emergency water supply, and EBMUD has 

tested the feasibility of artificial storage and recovery (ASR) 

of water through deep wells near the shore of San Francisco 

Bay, just south from San Lorenzo Creek (fig. 1; Luhdorff 

and Scalmanini Consulting Engineers, 2003). The EBMUD’s 

Bayside Groundwater Project (BGP) may ultimately include 

7 to 10 production/injection wells completed 500–650 ft 

below land surface, with groundwater extraction rates 

between 1 to 3 million gallons per day per well. During wet 

periods, EBMUD planned to inject treated surface water from 

reservoirs in the Sierra Nevada at a rate of about 1 million 

gallons per day per well and store it for use during droughts 

or times of surface-water scarcity (California Regional Water 

Quality Control Board, 2007). Projects operated by agencies 

in the Niles Cone and East Bay Plain groundwater subbasins 

may compete for limited groundwater storage capacity 

during wet periods, and because the subbasins may be 

hydraulically connected, recharged water may be extracted by 

nonparticipating agencies during dry periods.

Methods

Data collection included measurement of groundwater 

levels in wells; InSAR data compilation; streamflow 

measurements; measurements of physical parameters 

from streamflow and natural discharge; water-quality 

sample collection from 21 wells, 1 surface water site, and 

1 precipitation sampler; and collection of core material 

for mineralogical analysis. Groundwater-level data were 

collected in accordance with the protocols established by the 

“Groundwater Technical Procedures of the U.S. Geological 

Survey” (Cunningham and Schalk, 2011), which provides 

standardized technical procedures of many aspects of 

groundwater science, including site and measuring-point 

establishment and measurement of water levels (Wilde 

and others, 1999a, b). Water-quality data were collected 

in accordance with the protocols established by the USGS 

National Field Manual (Wilde and others, 1999a). The 

water-quality sampling protocols ensure that a representative 

sample is collected at each site and that the samples are 

collected and handled in a way that minimizes the potential for 

contamination of samples.

Groundwater-Level Measurement

Groundwater levels were measured by USGS and ACWD 

personnel in 21 wells perforated in the Deep aquifer and in 

24 wells perforated in the upper aquifer system during the 

spring and fall of 2002. All sites and water-level data were 

entered into the USGS National Water Information System 

(NWIS) database and are available from http://waterdata.

usgs.gov/nwis. Location, construction, and water-level data 

for wells measured as part of this study are provided in 

appendix 1.
8 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

InSAR Data Processing

InSAR imagery was processed and analyzed to 

measure the long-term surface displacement patterns and 

magnitudes within the Niles Cone and southern East Bay Plain 

groundwater subbasins. Shorter-term interferograms, maps 

of relative surface displacement constructed from InSAR 

data, were processed to assess if InSAR could be used to 

detect the effects of groundwater management strategies. The 

ACWD recharges groundwater through infiltration ponds and 

impoundments at Quarry Lakes Regional Park near Fremont, 

Calif. (fig. 1), near the apex of the Alameda Creek alluvial fan 

in the Niles Cone groundwater subbasin.

The synthetic aperture radar (SAR) data (radar scenes) 

used to construct the interferograms are from the SAR 

instrument on the European Space Agency ERS-2 satellite. 

The ERS-2 satellite has a steep look-angle (about 23° from 

vertical), which provides data sensitive to vertical deformation 

of the land surface (uplift and subsidence). The interferograms 

were constructed by the two-pass method using a USGS 

30-meter digital elevation model and both Diapason and 

GAMMA InSAR processing software packages (Centre 

National d’Etudes Spatiales, 1997; Werner and others, 2000). 

The images were processed using methods similar to those 

used by Stork and Sneed (2002). The resolution of a pixel in 

the interferograms is 323 square feet (ft2; 30 square meters). 

The interferogram measurements are range change (distance: 

positive, or uplift, and negative, or subsidence) in the radar 

line-of-sight, where one complete cycle of the color fringe 

(warm to cool) on the interferograms (the scale factor) is 

1.1 in. (28.3 mm). Under ideal conditions, it is possible to 

resolve changes in elevation on the order of 0.2 to 0.4 in. (5 to 

10 mm) at the scale of one pixel (Galloway and others, 2000).

Because of the high frequency of seismic activity in the 

densely populated San Francisco Bay area, scientists and 

government agencies are interested in monitoring techniques 

that provide information that may elucidate processes 

responsible for seismic geohazards. Each satellite can scan 

the same area every 35 days. Data were collected from 

January 1992 to May 1996 for ERS1 and from September 

1995 to 2003 for ERS2. Interpretation and construction of 

interferograms from ERS2 data after December 2002 were 

difficult owing to a gyroscope failure that caused the satellite 

to wobble at a level that limited interferogram generation. 

The two satellites are coordinated so that they can scan the 

same track and frame grid location at approximately the same 

local time, but with a temporal offset that varies by a number 

of days. Interferograms can be constructed from scenes from 

either or both satellites.

Streamflow Gains and Losses Estimation

To provide information needed to interpret results 

from groundwater-flow modeling by ACWD, the interaction 

between Alameda Creek and the adjacent aquifer was 

investigated by a reconnaissance-level survey of flow gains 

and losses along Alameda Creek in April 2002. Streamflow 

gains and losses were determined by a series of streamflow 

measurements between Rubber Dam No. 2 and the tidally 

affected stream reach downstream from USGS stream gage 

11180700 (Alameda Creek at Union City, Calif.; fig. 3). To 

assess chemical differences between stream water loss and 

groundwater, water temperature, pH, and specific electrical 

conductance were measured using standard field instruments 

and techniques (Wilde, 1998) at streamflow measurement 

sites and at three groundwater seeps and springs where they 

emerged from the flood plain and levee base. A potentiometric 

surface map (fig. 3) was constructed from water levels 

measured in ACWD observation wells monitoring the upper 

aquifer system (appendix 1) to provide information on the 

direction of groundwater flow in shallow sediments adjacent 

to Alameda Creek. The precipitation record from a nearby 

National Oceanic and Atmospheric Administration climate 

station (Newark, CA US) shows no precipitation in the area 

for at least 7 days prior to the streamflow measurements 

recorded on April 24, 2002 (https://www.ncdc.noaa.gov/

cdo-web/datasets/GHCND/stations/GHCND:USC00046144/

detail), and gage height measured in USGS gage 11180700 

(https://nwis.waterdata.usgs.gov/nwis/measurements/?site_

no=11180700&agency_cd=USGS&) remained consistent 

over the period of the survey (morning April 24, 2002, to 

midday April 25, 2002). The absence of precipitation and the 

consistency of the flow in Alameda Creek indicate that flows 

were stable in the studied reaches during the measurements 

and were therefore comparable between stations.

Most streamflow measurements were made using 

velocity-area methods (Rantz and others, 1982) using a Price 

pygmy current meter with a top setting wading rod. One day 

prior to velocity-area measurements, uniform-flow measuring 

sections were constructed by removing large cobbles from 

the stream bed and focusing flow to a single channel (where 

feasible) between parallel banks built using sand bags and 

planks. Where velocities were less than 0.2 feet per second 

(ft/s) and stream depths were less than 0.3 ft, streamflow 

measurements were made with modified 3-in. Parshall 

flumes. Flumes were used to measure small inflows from two 

tributary streams and were installed several hours prior to use. 

Streamflow measurements were rated from excellent to poor, 

depending on measurement technique and flow conditions. 

Poor ratings imply greater uncertainty and corresponded to 

measurements made with Price pygmy meters where stream 

depth and velocity approached the limitations of the method, 

less than 2 in. and 0.1 ft/s, respectively. Generally, streamflow 

measuring conditions were unsuitable in areas where water 

ponded behind stream channel vegetation or where the stream 

channel braided. Where feasible, streamflow measurement 

sites were selected in areas where sediment and vegetation had 

been recently removed by the Alameda County Flood Control 

and Water Conservation District to improve conveyance 

of winter storm flows. In the absence of these maintenance 

activities in Alameda Creek, it is likely that streamflow 

measurement would have been infeasible in most of the 

measured reaches.
Methods 9

SAC15-0557_fig 03

Alameda

Old

Alameda

Creek

HAYWARD FAULT

Quarry Lakes

Regional Park

Creek

Dry CreekDry Creek

Mowry 

well field RUBBER

DAM

NO. 2

RUBBER

DAM

NO. 1

Site 3

Site 2

Site 1

X’

X

Y

Y’

Site 6

Site 5

Z

Z’

Site 8

11180700

373630122010501

11180500

14L6

14.2

14D7

11.7

14H3

17.3

12K11

15.9

13E3

18.2

13P4

14R3 19.4

17.5

24F11

19.0

23J2

17.6

26K6

15.2

ARP 

wells

25D3

17.6

30E4

18.6

19N14

19.9

19E2

20.7

18R1

22.4

30A5

20.1

19J6

22.2

17M8

23.8

28D12

16.7

29A6

21.0 20R4

23.7

20H3

29.4

20J6

28.4

Site 9

Site 7

Site 4

29C8

21.2

Lago

Los

Osos

122°04' 122°02' 122°00'

37°

34'

37°

36'

EXPLANATION

Base modified from U.S. Geological Survey digital data, various scales

Lambert Conformal Conic projection

North American Datum of 1983 

0 0.5 1 MILE

0 0.5 1 KILOMETER

16

18

20

22

24

16

18

20

24

2220

Site 1

Upper aquifer system monitoring well, identifier, and water

 level altitude in feet above vertical datum (NAVD 88) 

Lakes and impoundments used for artificial recharge 

 of ground water

Gaining reach of Alameda Creek

Losing reach of Alameda Creek

Non gaining or losing reach of Alameda Creek

Tidally affected reach of Alameda Creek

Water-level altitude contour, in feet, in the upper aquifer system.

 Datum is the North American Vertical Datum of 1988 

 (NAVD 88).

Synoptic streamflow water-quality sampling site and 

 USGS site identifier

Streamflow measurement station and USGS site identifier

Synoptic streamflow measurement station and station 

 identifier

12

1180700

373630122010501

Municipal wells

18R1

11.5

Figure 3. Water-level elevation contours and water-level elevations in wells screened in the upper aquifer system, gaining and losing 

reaches along Alameda Creek, Quarry Lakes Regional Park recharge area, Alameda Creek, and Alameda County Water District (ACWD)

aquifer reclamation program (ARP) wells, Alameda County, California, April 2002.
10 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Water Sample Collection and Analysis

In this study, samples were evaluated for major ions, 

selected minor ions, selected trace elements, stable isotopes 

of water, and age-dating tracers to determine groundwater 

quality, the sources of high chloride water to wells, and 

the effects of managed aquifer recharge on groundwater of 

the Niles Cone and southern East Bay Plain groundwater 

subbasins. The spatial distribution of surface sources 

of industrial chemicals, such as volatile organic carbon 

compounds or trace elements, was not evaluated as part of this 

study.

Most samples collected as part of this study were from 

monitoring or production wells. Samples from monitoring 

wells in the Deep aquifer provide information on groundwater 

chemistry within the part of the Deep aquifer in which the 

monitoring well is screened and not necessarily for all of 

the Deep aquifer. Samples from production wells are a mix 

of groundwater that entered the well throughout the entire 

screened interval. As a result, it may be difficult to interpret 

samples collected from production wells that are screened 

in more than one aquifer. Samples also were collected from 

shallow monitoring wells (not in the Deep aquifer) in Deep 

aquifer recharge areas near Alameda Creek, Dry Creek, and 

Quarry Lakes at the head of the Alameda Creek alluvial fan. 

Comparisons of samples from the Deep aquifer and samples 

from shallow monitoring wells in recharge areas provide 

information on changes in groundwater chemistry and 

recharge age with depth.

Twenty-three water samples were collected from 

21 wells, 1 surface water site, and 1 precipitation sampler in 

the study area during 2002 to 2003. Water-quality samples 

were collected following the USGS field procedures outlined 

in the “U.S. Geological Survey Field Manual for Collection of 

Water Quality Data” (Wilde, 1999a). Samples were collected 

from production and monitoring wells after three casing 

volumes were removed from the well and field parameters 

stabilized. Existing pumps were used to collect samples from 

production wells. Temporary, positive-displacement sample 

pumps were used to collect samples from monitoring wells. 

Temperature, specific conductance, and pH were monitored 

in water from domestic, production, and monitoring wells 

during purging prior to sample collection. Sample collection, 

preservation, and analytical methods are given in appendix 2

at the back of this report. The precipitation sample is a 

composite of samples collected near Quarry Lakes from 

November 8, 2002, to June 5, 2003, and the stable-isotopic 

data can be considered as average values for winter and spring 

rainfall.

The field parameters temperature, specific conductance, 

pH, and alkalinity were measured at the time of sample 

collection using calibrated thermometers and portable meters. 

Meters were calibrated in the field prior to measurement. 

Dissolved oxygen also was measured in the field using the 

colorimetric indigo-carmine method just prior to sample 

collection. Water samples for analyses of major ions, nutrients, 

and selected trace elements were pressure-filtered in the field 

using capsule filters that had a pore size of 0.45 micrometer 

(μm). Samples for the laboratory analysis of pH and specific 

conductance were not filtered. 

Noble-gas samples were analyzed by the USGS Noble 

Gas Laboratory in Reston, Virginia, following the methods of 

Poreda and others (1988), Bayer and others (1989), Solomon 

and others (1992, 1996), and Beyerle and others (2000). 

Recharge temperatures and excess air concentrations were 

determined from dissolved Neon (Ne), Argon (Ar), Krypton 

(Kr), and Xenon (Xe) using methods described in AeschbachHertig and others (1999). Tritiogenic helium-3 (3

Hetrit) 

was computed as described in Solomon and Cook (2000). 

Water samples for carbon isotopes and carbon-14 activities 

were analyzed by the University of Waterloo laboratory 

under contract with the USGS using mass spectroscopy and 

accelerator mass spectroscopy, respectively.

Statistical analysis of constituents was done using 

Kruskal-Wallis rank sum tests [kruskal.test(x, g)] in the 

computer program R (R Development Core Team, 2008). 

The Kruskal-Wallis test is used when there is one nominal 

variable and one measurement variable, and it does not 

require assumptions about the specific shape of the probability 

distribution. Data are ranked based on their measurement 

value from smallest to largest before the test statistic is 

calculated. The loss of information due to substituting ranks 

for original data make the test less powerful; however, data 

do not need to be normally distributed as in an analysis of 

variance (ANOVA) test. Small P-values (less than 0.05) at a 

significance level of 95 percent show that differences in the 

distribution of data between two or more groups are not due to 

random sampling error only, but in fact that at least one group 

has a statistically significant difference in the distribution; 

conclusions about the differences in the distribution of data 

cannot be made with P-values of 0.05 or greater.

Collection and Analysis of Core and Cuttings 

Material

Mineralogic analyses were done on four samples 

collected by drilling and coring. Drill cuttings and core 

material were collected from well 14D3 and of a composite 

of coarse-grained outcrop material at Quarry Lakes recharge 

pond. The elemental composition of cores and cuttings was 

determined by inductively coupled plasma–mass spectrometry 

(ICP–MS; Briggs and Meier, 2002). The mineralogy of 

selected cores and cuttings was determined by X-ray 

diffraction (Amonette and Zelazny, 1994). Images of selected 

materials were obtained using a scanning electron microscope 

equipped with a spectral analyzer to determine the primary 

or secondary minerals that might participate in dissolutionprecipitation reactions as groundwater interacts with sediments 

in the aquifer system and to determine the uranium and 

thorium composition of aquifer materials (Amonette and 

Zelazny, 1994). Information about the collection and analysis, 

as well as results from the analysis, is provided in appendix 3.
Hydrogeology 11

Hydrogeology

Data and various analyses were used to evaluate the 

effect of groundwater management practices on the aquifer 

systems and movement of water through the Deep aquifer, 

including between subbasins. This section of the report 

presents and discusses results for groundwater movement, 

vertical displacement of the land surface, and streamflow gains 

and losses in the recharge area near the apex of the Alameda 

Creek alluvial fan.

Groundwater Movement

Water-level contours indicate that groundwater generally 

flows from the eastern recharge areas at Quarry Lakes and 

Alameda Creek to the north and west (figs. 3 and 4). Closely 

spaced contours to the south in the Deep aquifer (fig. 4) are 

the result of pumping from the nearby Mowry well field and 

Aquifer Reclamation Program (ARP) wells. Water-level data 

from wells completed solely in the upper aquifer system to 

the north of Old Alameda Creek were unavailable because 

the deposits that compose the upper aquifer system in this 

area are finer-grained, yield less water to wells than deposits 

to the south, and therefore, are not ideal locations for wells. 

Measurements collected in 2002 show that the elevation of 

water levels in wells completed in the upper aquifer system 

(wells 4S/1W-17M7, -17M8; 4S/2W-12K9, -12K10, -12K11; 

4S/2W-13P4, -13P6, -13P7; and 4S/2W-14D5, -14D6, -14D7) 

were as much as 20 ft higher than water levels in wells 

completed in the Deep aquifer (wells 4S/1W-17M6; 4S/2W12K8; 4S/2W-13P5, and 4S/2W-14D3, -14D4; appendix 1).

Water levels in the Deep aquifer indicate groundwater 

flows to the west and north from Quarry Lakes (fig. 4). The 

groundwater flowpath B–B' follows this general northwest 

trend and was used for the purpose of geochemical modeling 

described later in this report (fig. 4). Water-level elevation in 

the Deep aquifer were below sea level in most of the area, as 

low as about –9 ft in well (3L1) in the southern East Bay Plain 

groundwater subbasin within the transition zone (table 1–1). 

Water-level contours indicate that flow of groundwater in 

the Deep aquifer in 2002 was from recharge areas near the 

head of the alluvial fan of Alameda Creek to the southern 

East Bay Plain groundwater subbasin. The effects of tides 

in San Francisco Bay on groundwater levels in the Deep 

aquifer were not considered in figure 4. The effects of tidal 

loading on groundwater levels in the southern East Bay Plain 

groundwater subbasin measured by Izbicki and others (2003) 

show water levels in the Deep aquifer can change by more 

than 1.5 ft in a 6-hour period. 

The velocity and volume of the flow within the Deep 

aquifer, being dependent on the hydraulic gradient, may have 

increased since ACWD’s managed aquifer recharge activities 

raised groundwater levels near Quarry Lakes. 

Under predevelopment conditions, the quantity of groundwater 

flowing to the northwest may have been substantially less 

than under conditions in 2002. During the mid-1900s when 

pumping was greater and water-level elevation dropped 

in some places to more than 100 ft below sea level, the 

magnitude and the direction of groundwater flow in the Deep 

aquifer was likely substantially different than today, either 

moving with less velocity toward the northwest or, in parts of 

the study area, even moving west to east from San Francisco 

Bay (California Department of Water Resources, 1963). 

Local Short-Term Land-Surface Displacement

Beginning in the winter–spring of 1995, in preparation 

for pond reconstruction, ACWD reduced water volume in the 

ponds at Quarry Lakes Regional Park and increased pumping 

at Aquifer Reclamation Program (ARP) wells, lowering water 

levels in wells in both the upper aquifer system and the Deep 

aquifer (fig. 5). From April 10, 1997, to July 29, 1997, ACWD 

dewatered the ponds by pumping about 7,700 acre-ft of pond 

water to Alameda Creek. After reconstruction, the ponds were 

filled to capacity with local runoff from the Alameda Creek 

watershed, and ARP well pumpage was reduced (fig. 5). 

Above-average rainfall during fall 1997 and winter 1998 

contributed to the availability of water from Alameda Creek 

for groundwater recharge (fig. 5). Groundwater levels in wells 

in the shallow aquifer system and the Deep aquifer underlying 

the Niles Cone groundwater subbasin increased about 20 ft 

during summer 1997–winter 1998 (fig. 5). InSAR was used 

to monitor land-surface displacement caused by pumping and 

subsequent recharge to the aquifer system.

Two independent interferograms span the period of the 

refilling of the ponds (fig. 6); both interferograms indicate 

that as much as 0.8 in. (21 mm) of uplift, relative to uplift 

occurring at the ponds, occurred during this period in the 

area west from the ponds. The July 17, 1997, to March 19, 

1998, interferogram shows a broad uplift feature in distal 

(lower) parts of the Alameda Creek alluvial fan, west from the 

Quarry Lakes infiltration ponds. Maximum relative uplift is 

about 0.8 in. (21 mm). The localized area of maximum uplift 

to the west of Quarry Lakes may reflect the lithology of the 

alluvial fan of Alameda Creek. Relative uplift was greater in 

distal parts of the alluvial fan west of the ponds where finergrained (clayey) deposits, which are more compressible and 

expandable than sand-and-gravel layers, compose a greater 

proportion of the sediments. Relative uplift was less (about 

0.4 in. [10 mm]) in the fan near the ponds, which is composed 

of coarser-grained sediments. Increased hydraulic head from 

rising groundwater levels caused by pond refilling would be 

expected to translate rapidly through permeable coarse-grained 

parts of the aquifer system and then diffuse vertically into 

finer-grained, expandable deposits and clayey layers. 
12 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

SAC15-0557_fig 04 Add this to figure caption, Aquifer restoration program (ARP)

B Hayward

Fremont

880

880

92

84

Alameda

Creek

Creek

Dry

Alameda

Old

Quarry Lakes

Regional Park

Creek

San Francisco

Bay

Mowry

well field

B’

HAYWARD FAULT

MISSION FAULT

0 1 2 MILES

0 1 2 KILOMETERS

Background image is the intellectual property of Esri and is used herein under license.

Copyright © 2014 Esri and its licensors. All rights reserved. Base modified from U.S.

Geological Survey digital data, various scales; Lambert Conformal Conic projection;

North American Datum of 1983

37°38'

37°36'

37°34'

EXPLANATION

B B’

Water-level altitude contours in feet above the North

 American Vertical Datum of 1988 (NAVD 88)

Deep aquifer monitoring well, identifier, and

 water-level altitude in feet above NAVD 88

Municipal wells

Transition zone (Luhdorff and Scalmanini

 Consulting Engineers, 2003)

Tidally influenced wetlands

Faults

Flowpath for geochemical analyses

0

2

1

37°32'

DIABLO RANGE

ARP wells

-1

-2

122°10 122°08' 122°06' 122°04' 122°02' 122°00'

29L6

0.6

32D2

−5.7

4R1

−2.4

10E4

−1.4

35J11

−4.5

3L1

−9.1

15L5

−1.4

14D4

−1.5

12K8

−0.9 7P4

−0.1

17M6

2.1

13P5

1.6

26K4

0.4

25D1

0.0 30E3

−0.2

30A2

−0.4

28D1

−1.3

30E3

−0.2

Figure 4. Water-level elevation contours and water-level elevations in wells screened in the Deep aquifer; Quarry Lakes Regional 

Park recharge area; Alameda Creek; and Alameda County Water District (ACWD) Aquifer Reclamation Program (ARP) wells, Niles Cone 

groundwater subbasin, Alameda County, California, 2002.
Hydrogeology 13

SAC15-0557_fig 05

55

60

65

70

75

80

85

90

95

20

25

30

35

40

45

50

55

Deep aquifer well

upper aquifer system well

San Francisco International Airport (SFO WSP AP)

Quarry Lakes (Lago Los Osos)

Aquifer Reclamation Program (ARP) wells

4S/2W-12C1

4S/2W-13R7

January

1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

January

1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

January

1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

January

1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

January

1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

2,500

2,000

1,500

1,000

500

0

Volume pumped,

in acre feet per month

Depth below land surface,

in feet

Depth below land surface,

in feet

35

30

25

20

15

10

5

0

−5

−10

Water surface elevation, 

in feet above mean sea level

14

12

10

8

6

4

2

1

Precipitation, in inches per month

Figure 5. Precipitation at San Francisco International Airport, water-level elevation at infiltration pond Lago Los Osos, total pumpage 

from Alameda County Water District’s Aquifer Reclamation Program (ARP) wells, and groundwater elevations in selected wells north 

from Alameda Creek in the Niles Cone groundwater subbasin, Alameda County, California. The highlighted areas mark the (green) period 

for the interferogram shown in figure 6A (July 17, 1997, to March 19, 1998) and (blue) period for the interferogram shown in figure 6B

(September 6, 1997, to May 9, 1998).
14 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

SAC15-0557_fig 6AB add ‘in., inches; mm, millimeters’ to figure caption

Water bodies

!

!

!

!

!

!

!

B

September 6, 1997, to May 9, 1998

A

July 17,1997, to March 19, 1998

0 1 2 MILES

0 1 2 KILOMETERS

4S/2W-12C001

4S/2W-13R007

4S/2W-12C001

4S/2W-13R007

~0.7 in. relative uplift

~1.1 in. relative uplift

~0.4 in. relative uplift

~0.8 in. relative uplift

−122°03' −122°01' −121°59' −121°57' −121°55'

−122°03' −122°01' −121°59' −121°57' −121°55'

 37°37'

 37°36'

 37°35'

 37°34'

 37°33'

 37°32'

 37°31'

 37°30'

 37°37'

 37°36'

 37°35'

 37°34'

 37°33'

 37°32'

 37°31'

 37°30' 0 1.1 in.

(28 mm)

0.8 in.

(21 mm)

−0.7 in.

(−17 mm)

−1.1 in.

(−28 mm)

Relative

Subsidence Uplift

EXPLANATION

Quarry Lakes

Regional Park

Quarry Lakes

Regional Park

Figure 6. InSAR interferogram displaying relative subsidence or uplift in the Niles Cone groundwater subbasin during refilling of 

infiltration ponds at Quarry Lakes Regional Park, Alameda County, California. A, July 17, 1997, to March 19, 1998; B, September 6, 1997, to 

May 9, 1998. [Abbreviations: in., inch; mm, millimeter; ~, about].
Hydrogeology 15

Similar relative uplift south of Quarry Lakes is indicated 

on the September 6, 1997, to May 9, 1998, interferogram; 

however, a region of relative subsidence is indicated southwest 

(band of dark blue between Quarry Lakes and the region of 

uplift) from Quarry Lakes (fig. 6B). The uplift feature on this 

interferogram is likely a continuation of the uplift seen on 

the previous interferogram that has increased in magnitude 

from March (the end date of the first interferogram, fig. 6A) 

to May (the end date of the second interferogram, fig. 6B) 

as the hydrostatic pressure from recharging water continued 

to propagate from the ponds. The subsidence feature is 

likely due to pumping of groundwater wells in the area, as 

the interferogram extends into May, which is within the 

beginning of the pumping season. Incoherent areas (areas of 

indiscernible color on figures 6A and 6B) in the western parts 

of the interferogram limit interpretation of the data in this area. 

The magnitude of relative uplift west from the recharge 

ponds is reasonable for elastic expansion of sedimentary 

materials experiencing an increase in hydraulic head similar 

to that resulting from pond refilling. Calculated expansion 

for 600 ft of unconsolidated sediment after a 20-ft increase 

of hydraulic head ranges from 0.3 to 1.1 in. (7 to 29 mm) 

for aquifer-system specific storage values ranging from 

2 × 10–6 ft–1 to 8 × 10–6 ft–1, respectively (Francis Riley, USGS 

emeritus, written commun., 2004). Uncertainties regarding the 

mechanical properties and thickness of sedimentary deposits 

of the aquifer system preclude estimating a narrower range 

of likely uplift and complicate the assessment of differences 

in range change indicated on the interferograms. Elastic 

compaction of the aquifer system that occurred when ACWD 

lowered groundwater levels by about 20 ft in the Niles Cone 

groundwater subbasin prior to construction at the infiltration 

ponds (winter 1995–fall 1997) could have produced land 

subsidence of a magnitude similar to expansion of the 

aquifer indicated on the interferogram (fig. 6); unfortunately, 

compatible data bracketing the period of water-level decline 

are unavailable.

Streamflow Gains and Losses in Alameda Creek

Gaining and losing sections of Alameda Creek (fig. 3) 

were determined using streamflow measurements (fig. 7), 

along with comparisons of stream channel bathymetry with 

water levels from adjacent wells (fig. 8). Streamflow data 

are presented in appendix 4. The reach between site 1 and 

site 5 is generally a losing reach, and streamflow along this 

reach decreases with increasing distance downstream. The 

water level measured in well 4S/2W-19J6, located southwest 

of the channel just downstream from site 3, is lower in 

elevation than the thalweg of the channel (fig. 8A). Water 

from this reach likely recharges the upper aquifer system 

and the Deep aquifer because of the hydraulic connection 

between the two near Quarry Lakes. The reach from site 

6 to just downstream of site 9 is gaining where the mound 

caused by groundwater recharge at Quarry Lakes intersects 

the stream, and streamflow along this reach increases with 

increasing distance downstream. Comparisons of two channel 

cross sections along the reach, between site 6 and site 9, 

with adjacent wells, one north of the channel (4S/2W-14H3) 

and one south of the channel (4S/2W-13E3; fig. 8B), show 

that water levels in the wells are higher in elevation than the 

thalweg of the channel. Additional groundwater discharge, in 

the form of seeps and springs, were present along this reach. 

Streamflow was measured during a low-flow period, and 

stream stage data from nearby gage 11180700 suggest that 

during high winter flows the reach between site 6 and site 9 

may be losing. The seepage run results suggest that during 

the summer low-flow period, Alameda Creek gains about 

3.5 cubic feet per second (cfs) between sites 6 and 9. This 

equates to about 1,270 acre-ft/yr, or about 4 percent of the 

30,000 acre-ft/yr estimated to be infiltrated (“Groundwater 

Management” section), about 5 percent of local groundwater 

pumping of 24,000 acre-ft/yr, and about 13 percent of 

pumping at the ARP wells of 10,000 acre-ft/yr.

The water temperature in Alameda Creek was 

measured at each stream gaging site (fig. 7) and ranged 

from 19 °C at site 1 to 23 °C at site 5 and averaged 21.3 °C. 

Water temperature in Alameda Creek was greater than the 

historical average summer temperature of the area, 18 °C, 

and was generally warmest downstream from Quarry Lakes. 

Temperature decreased in the downstream (between sites 6 

and 9) gaining reaches of Alameda Creek as a result of 

groundwater discharge.
16 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

SAC15-0557_fig 07

0

1

2

3

4

5

Streamflow, in cubic feet per second Water temperature, in degrees centigrade

A. April 24, 2002, morning

B. April 24, 2002, afternoon

C. April 25, 2002, midday

D. April 25, 2002, midday

0

1

2

3

4

5

0

25

23

21

19

17

15

1

2

3

4

5

4 3 2 1 0

Distance, in miles downstream from site 1 at Rubber Dam No. 2

4

4

1

2

3

8

8 7

9

9

6

6

5

1

9

7

6 5 2 1

9

8

7 6 5

4

2

1

Streamflow, in cubic feet per second Streamflow, in cubic feet per second

Figure 7. Streamflow and water-temperature measurements along Alameda Creek, April 24–25, 2002, Alameda County, California.
Hydrogeology 17

SAC15-0557_fig 08abc

 

15.0

15.5

16.0

24 25 26 27 28

2002

29 30 1 2

 Water-level altitude,

in feet above sea level

Thalweg altitude 7.7 feet

April May

X X’

South North

South North

South North

A

B

0

10

20

30

40

50

60

Altitude, in feet above mean sea level

Altitude, in feet above mean sea level Altitude, in feet above mean sea level

−200 −100 0 100 200

Distance, in feet from flood channel centerline

Distance, in feet from flood channel centerline

−200 −100 0 100 200 300 400

Distance, in feet from flood channel centerline

−200 −100 0 100 200

C

Land surface altitude from topographic 

survey by Alameda County Flood Control 

and Water Conservation District, written 

commun., 2002

Water level May 1, 2002, 

19.45 feet above mean 

sea level

Depth 125 feet

Perforated interval –27.6 to

–94.6 feet above mean sea level

Perforated interval −37.1 to −92.1 feet above mean sea level

Depth 125 feet

Perforated interval unknown

4S/2W-19J6

Approximate altitude determined 

from U.S. Geological Survey (USGS) 

7.5-minute topographic map 

Thalweg altitude 21.7 feet 

Land surface altitude from topographic survey 

by Alameda County Flood Control and Water 

Conservation District, written commun., 2002

Land surface altitude from topographic survey 

by Alameda County Flood Control and Water 

Conservation District, written commun., 2002

Approximate altitude 

determind from USGS

7.5-minute topographic 

map

Approximate altitude determind 

from USGS 7.5-minute 

topographic map

Y Y’

Z Z’

Thalweg altitude 9.9 feet

4S/1W-13E3

4S/1W-13E3

0

10

20

30

40

0

10

20

30

40

Water level May 2, 2002, 14.6 feet 

above mean sea level

4S/2W-14H3

Figure 8. Cross-sectional bathymetry of Alameda Creek. A, along section X–X’ with water-level elevation in adjacent well 4S/2W-19J6; 

B, along section Y–Y’ with water-level elevation in adjacent well 4S/1W-13E3; and C, along section Z–Z’ with water-level elevation in 

adjacent well 4S/2W-14H3, Alameda County, California.
18 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Geochemistry

This section begins with results and discussion of the 

groundwater chemistry in general and then continues with 

additional geochemical insights provided by analyses of ionic 

composition, a mixing model for a diagnostic ionic ratio, and 

analyses of noble gases, tritium, and other isotopes of water 

and dissolved carbon.

Chemistry of Groundwater

Chemistry of water in aquifers underlying the Niles 

Cone and southern East Bay Plain groundwater subbasins 

is influenced by the chemistry of the natural and managed 

aquifer recharge water and the geochemical reactions that 

occur within the aquifer system. Also, intruding seawater, 

mixing with water from surrounding and underlying 

deposits, or mixing with water from estuarine deposits 

near San Francisco Bay, may alter groundwater chemistry, 

increase chloride concentrations, and degrade the quality 

of groundwater. Flow from shallow aquifers into deeper 

aquifers occurs naturally along the eastern boundary of the 

study area, along the Hayward Fault, and also through the 

failed and leaking casings of abandoned wells (San Francisco 

Bay Regional Water Quality Control Board, 1999). Waterlevel elevation data are consistent with recharge from the 

Quarry Lakes Regional Park infiltration ponds reaching the 

upper aquifer system and the Deep aquifer in the immediate 

vicinity. Seawater intrusion in aquifers underlying the Niles 

Cone and southern East Bay Plain groundwater subbasins 

has been a problem since the late 1800s and was extensively 

studied in the early 1960s by the California Department of 

Water Resources (1960, 1963). Results of chemical analysis 

of 23 samples from 15 deep wells, 6 shallow wells, 1 stream, 

and 1 precipitation station collected by the USGS are given 

in appendix 5 at the back of this report. In addition, water 

chemistry results from a depth-dependent sample taken at 

910 ft from 2S/3W-19Q3 (Izbicki and others, 2003) in the 

East Bay Plain groundwater subbasin are displayed in figures 

along with results from this study representing water from 

deep, consolidated sediments (connate water) adjacent to San 

Francisco Bay.

Physical Properties and Chemical 

Characteristics of Groundwater

The physical properties and the chemical characteristics 

of water from wells perforated in the upper aquifer system 

are different from those of water from wells perforated in the 

Deep aquifer (fig. 9). Infiltration of recharge water at Quarry 

Lakes has influenced the chemistry of water in nearby wells. 

In addition, water-chemistry data suggest that groundwater 

from wells may have been affected by seawater intrusion or 

mixing with poor-quality, high-chloride water from finegrained estuarine deposits near San Francisco Bay.

The field pH of water sampled from the upper aquifer 

system and the Deep aquifer ranged from 6.9 to 7.2 and 

7.2 to 8.6, with median pH of 7.1 and 7.5, respectively. 

The highest pH was in water from monitoring well 4S/2W14D3 completed in the Deep aquifer 400 to 450 ft below 

land surface. The pH of groundwater from the Deep aquifer 

was significantly higher than the pH of groundwater from 

the upper aquifer system (P-value = 0.0007). In siliciclastic 

aquifers, groundwater pH increase from slightly acidic to 

neutral pH near recharge sources to more alkaline values with 

depth and distance along the groundwater flowpath as a result 

of primary mineral dissolution (feldspars and micas; Izbicki 

and others, 1992, 2003).

Dissolved solids (as measured by residue on evaporation) 

of water sampled from wells in the upper aquifer system and 

Deep aquifer ranged from 420 to 880 milligrams per liter 

(mg/L) and 350 to 1,080 mg/L, with median concentrations 

of 590 and 480 mg/L, respectively. Higher dissolved solids in 

groundwater from the Deep aquifer were generally associated 

with higher chloride concentrations. Two monitoring wells in 

the Deep aquifer, 4S2W-15L5 and 4S/2W-13P5, had dissolved 

solids concentrations of 880 and 1,080 mg/L, respectively, and 

chloride concentrations of 346 and 315 mg/L, respectively. 

These wells represent water that has mixed with high-salinity 

water intruded from San Francisco Bay and has dissolved 

solids and chloride values that are not representative of 

the aquifer systems; to avoid skewing the data, they were 

excluded from analyses of dissolved solids and chloride 

data. Excluding wells impacted by high-chloride water 

(>250 mg/L), the median dissolved-solids concentration was 

significantly higher in water from wells in the upper aquifer 

system (fig. 9) than in water from wells in the Deep aquifer 

(P-value = 0.0085). Higher dissolved solids concentrations in 

some of the upper-aquifer-system wells may reflect changes 

in recharge water chemistry as the Alameda Creek watershed 

has become more urbanized in recent years, increasing 

anthropogenic effects on water chemistry. Alternatively, the 

lower dissolved-solids concentrations in the Deep aquifer 

could be the result of geochemical reactions that remove 

constituents from groundwater, such as sulfate through sulfate 

reduction under reduced conditions, or calcium and sodium 

through cation exchange (fig. 10), as will be discussed in the 

“Major-Ion Composition” section below.
Geochemistry 19

SAC15-0557_fig 09

6

6

7

8

9

Standard units

pH

Upper aquifer

system

6 15

Deep aquifer

6 15

Upper aquifer

system

Deep aquifer

Dissolved oxygen

Milligrams per liter

0

1

2

3

4

5

Dissolved solids

6 15

Upper aquifer

system

Deep aquifer

Milligrams per liter

6 15

Upper aquifer

system

Deep aquifer

Milligrams per liter 100

0

200

300

400

500

Calcium

6 15

Upper aquifer

system

Deep aquifer

Milligrams per liter

Sodium

0

100

200

300

400

500

6 15

Upper aquifer

system

Deep aquifer

Milligrams per liter, as nitrogen

0

2

4

6

8

10

Nitrate

6 15

Upper aquifer

system

Deep aquifer

Milligrams per liter

Chloride

100

0

200

300

400

500

6 15

Upper aquifer

system

Deep aquifer

Milligrams per liter, 

as calcium carbonate (CaCO3

)

Alkalinity

100

0

200

300

400

500

6 15

Upper aquifer

system

Deep aquifer

Milligrams per liter

Sulfate

100

0

200

300

400

500

6 15

Upper aquifer

system

Deep aquifer

Micrograms per liter

Iron

0

100

200

300

400

500

6 15

Upper aquifer

system

Deep aquifer

Micrograms per liter

Manganese

0

100

200

300

400

500

0

200

400

600

800

1,000

1,200

EXPLANATION

95th percentile

Number of samples

75th percentile

50th percentile

(median)

25th percentile

5th percentile

Differences in values between the Upper aquifer 

system and the Deep aquifer are significantly 

different based on the Kruskal-Wallis rank 

sum tests.

α=0.05

Figure 9. pH, dissolved oxygen, and selected major-ion, nutrient, and trace-element concentrations in water from wells sampled in the 

Niles Cone and southern East Bay Plain groundwater subbasins, Alameda County, California, 2002–03.
20 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

SAC15-0557_fig 10

Upper aquifer system wells

Deep aquifer wells

Well 19Q3 (Izbicki and others, 2003) 19Q3

EXPLANATION

13P6

1

2

3

1 Wells near recharge areas along mountain front

2 Increasing chloride concentrations and cation exchange—

 Wells affected by seawater intrusion and mixing with high-

 chloride water from fine-grained deposits

3 Calcite precipitation and cation exchange—Deep wells and

 wells at the downgradient end of long flow paths

 20 

 40 

 60 

 80 

 100 

Calcium

Magnesium

Sodium plus potassium

 20 

 0 

 40 

 60 

 80 

 100 

 100 

 80 

 60 

 40 

 20 

 0 

Sulfate

 100 

 80 

 60 

 40 

 20 

 0 

 0 

 20 

 40 

 60 

 80 

 100 

 0 

 20 

 40 

 60 

 80 

 100 

Chloride, fluoride, nitrite plus nitrate

Carbonate plus bicarbonate

Sulfate plus chloride

Calcium plus magnesium

 100 

 80 

 60 

 40 

 20 

 0 

 100 

 80 

 60 

 40 

 20 

 0 0 

 20 

 40 

 60 

 80 

 100 

 100 

 80 

 60 

 40 

 20 

 0 

 0 

PERCENT

PERCENT

PERCENT

19Q3

13P6

17M8

13P7

13P4

17M7

12K10

13P5

17M6

10E4

15L5

14D4

29L6

14D3

4E1

4E1

4R1

12C1

4F3

2H1

3L1

20L20

12K8

Figure 10. Major-ion composition of samples from selected wells in the Niles Cone and southern East Bay Plain groundwater 

subbasins, Alameda County, California, 2002–03.
Geochemistry 21

Water from wells sampled in the upper aquifer system 

was both oxic (>0.30 mg/L) and suboxic (<0.30 mg/L; Tiedje, 

1988), with dissolved oxygen concentrations ranging from 2.9 

to 0.2 mg/L, whereas water from wells in the Deep aquifer 

was generally reduced, with dissolved oxygen concentrations 

no greater than 1 mg/L. The dissolved oxygen concentrations 

of water from sampled wells in the Deep aquifer were 

significantly less than the concentrations in water from wells 

in the upper aquifer system (P-value = 0.0025). Differences 

in oxidation-reduction (redox) conditions between the upper 

aquifer system and the Deep aquifer may explain significantly 

lower concentrations of nitrate (P-value = 0.0124) and higher 

concentrations of manganese (P-value = 0.0005) and iron 

(P-value = 0.0325) in water from wells in the Deep aquifer 

compared to the upper aquifer system. Although no wells 

exceeded the EPA drinking water maximum contaminant 

level (MCL) for nitrate of 10 mg/L as nitrogen, two wells 

completed in the upper aquifer system near recharge areas at 

Quarry Lakes and along Alameda Creek, 4S/2W-12K10 and 

4S/2W-13P7, had nitrate concentrations of 8.1 and 9.5 mg/L 

as nitrogen, respectively. Similar to dissolved solids, higher 

nitrate concentrations in water from these wells also could 

result from changing land use and increased urbanization in 

the Alameda Creek watershed; specific sources may include 

agricultural or residential fertilizer use and septic discharges. 

Major-Ion Composition

The major-ion composition of water from sampled 

wells was evaluated using a Piper (trilinear) diagram. A Piper 

diagram (Piper, 1944) shows the relative contribution of 

major cations and anions, on a charge-equivalent basis, to the 

total ionic content of the water. Percentage scales along the 

sides of the diagram indicate the relative concentration, in 

milliequivalents per liter, of each major ion. Cations are shown 

in the left triangle and anions are shown in the right triangle; 

the central diamond integrates the data.

Water from upper-aquifer-system wells located near 

Quarry Lakes, 4S/2W-13P4, 13P6, 13P7; 4S/1W-17M7–8; and 

4S/2W-12K10, has a major-ion composition marked by higher 

calcium and magnesium percentages than water from most 

wells in the Deep aquifer (fig. 10). These wells are possibly 

influenced by water recharged at Quarry Lakes, as well as 

water from the ponded areas behind the inflatable dams in 

Alameda Creek. Most water from wells in the Deep aquifer 

plot below data from the upper aquifer system on figure 10, 

because of an increase in sodium relative to calcium plus 

magnesium and an increase in bicarbonate as water flows 

through the aquifer. In coastal aquifers in California, including 

the East Bay Plain groundwater subbasin, similar trends have 

been attributed to precipitation of calcite and (or) exchange 

of calcium and magnesium for sodium on clay within aquifer 

deposits and dissolution of carbonate minerals, respectively 

(Izbicki and others, 1992, 2003). Water from wells 13P5, 

17M6, and 4S/2W-10E4 in the Deep aquifer has elevated 

chloride concentrations and plots along a line above and to the 

right of data from the upper aquifer system in figure 10. This 

pattern is characteristic of groundwater intruded by seawater 

(Piper and Garrett, 1953; Izbicki, 1996; Izbicki and others, 

2003) and is the result of the exchange of sodium for calcium 

and magnesium on clay in aquifer deposits. Similar patterns 

have been observed in the East Bay Plain groundwater 

subbasin (Muir, 1997; Izbicki and others, 2003). Water from 

well 4S/2W-15L5 has major-ion proportions similar to well 

2S/3W-19Q3, which yields water from partly consolidated 

sediments underlying freshwater aquifers of the East Bay Plain 

groundwater subbasin (Izbicki and others, 2003), suggesting 

the source of high-chloride water to well 15L5 is likely from 

partly-consolidated marine rock.

Chloride-to-Iodide Ratios

Use of certain minor ions and trace elements to 

determine the source of high-chloride water to wells in the 

Long Beach and Santa Ana areas of southern California was 

demonstrated by Piper and Garrett (1953). Other studies 

have applied these techniques to the study of the source and 

movement of seawater and other brines in aquifers (Jones and 

Garbarino, 1999; Izbicki, 1996; Izbicki and others, 2003), 

and increasingly refined approaches have been developed 

to distinguish mixtures of native (fresh) water and seawater 

from mixtures of native water and high-chloride water from 

underlying partly consolidated rock in coastal California 

aquifer systems (Izbicki, 1991; Izbicki, 1996). In this report, 

chloride-to-iodide ratios were used to determine the source of 

high-chloride water to wells and to evaluate the geochemical 

evolution of water as it flows through unconsolidated deposits 

underlying the Niles Cone and southern East Bay Plain 

groundwater subbasins (fig. 11).

Chloride is highly soluble and not readily sorbed on 

mineral surfaces or organic material. In addition, with the 

exception of evaporite salts, chloride does not occur at high 

concentrations in most rock-forming minerals or aquifer 

materials (Feth, 1981; Davis and others, 1998). 

Iodide is affected by biological and redox processes and 

is reactive in groundwater systems. Iodide concentrations 

in seawater are low, about 0.06 mg/L; however, iodide 

concentrations in marine rocks and unconsolidated material 

deposited in marine environments are elevated relative to 

seawater and nonmarine materials owing to concentration 

of iodide from seawater by nearshore marine vegetation 

(Hem, 1985). Previously reported iodide concentrations in 

high-chloride water from marine rocks that surround and 

underlie coastal aquifers in California are as high as 2.4 mg/L 

(Izbicki and others, 2003). Iodide concentrations in highly 

concentrated brines from some deep wells can be as high 

as 46 mg/L (Hem, 1985). Ratios are especially sensitive to 

mixing, and the addition of a small volume of water having 

different chloride and trace-element compositions may 

produce a large change in the trace-element-to-chloride ratio 

of water from a well.
22 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Iodide concentrations in water from wells underlying 

the Niles Cone and southern East Bay Plain groundwater 

subbasins ranged from 0.002 to 0.632 mg/L. Chloride-toiodide ratios in wells in the upper aquifer system ranged 

from 7,600 to 135,000 (fig. 11). For waters having chloride 

concentrations below 250 mg/L (about 8 millimoles per 

liter; fig. 11), higher chloride-to-iodide ratios are typical in 

water from alluvium eroded from granitic terrain and from 

Franciscan rocks (Izbicki, 1991; Izbicki, 1996). The chlorideto-iodide ratios for water from wells 4S/1W-17M8 and 4S/2W13P4, the uppermost wells near Quarry Lakes, are lower than 

those of the three other upper-aquifer-system wells in the area 

with data (fig. 11). These ratios are probably representative 

of the water recharged at Quarry Lakes, owing to the close 

proximity to Quarry Lakes and shallow screens of the wells. 

Other upper-aquifer-system wells near the recharge area plot 

along a line representative of mixing of recharge through local 

rivers and streams, represented by a Dry Creek sample, and 

seawater (Hem, 1985). 

Water from most wells screened in the Deep aquifer has 

a chloride-to-iodide ratio around 1,000, typical of alluvial 

deposits weathered from marine rocks and water from partly 

consolidated marine rock (Piper and Garrett, 1953; Izbicki, 

1991; Land and others, 2002). The chloride-to-iodide ratio is 

greatest in Deep aquifer well 13P5, with a value of 560,000, 

and plots slightly above the seawater mixing line (fig. 11). 

SAC15-0557_fig 11

Dry Creek

Brine (Hem, 1985)

Seawater (Hem, 1985)

250 mg/L

10 100 1,000 10,000 100,000

100

1,000

10,000

100,000

1,000,000

10,000,000

1,000 10,000

Chloride to iodide molar ratio

Chloride concentration, millimoles per liter

EXPLANATION

Upper aquifer system

Deep aquifer

Well sampled by Izbicki and others, 2003

Surface water

Seawater

Average composition of brines from partly consolidated rocks defined by Hem, 1985

Seawater mixing lines

Brine mixing line

0.1 1 10 100

Chloride concentration, in milligrams per liter

 13P7

 13P4

 17M8

 17M8

13P5

15L5

19Q3

12K8

15L5

19Q3

Figure 11. Chloride-to-iodide ratios as a function of chloride concentration in water from wells, Niles Cone and southern East Bay 

Plain groundwater subbasins, Alameda County, California, 2002–03.
Geochemistry 23

Water in this well is likely influenced by past seawater 

intrusion. The highest iodide concentration (0.632 mg/L) was 

in the water collected from well 4S/2W-15L5. The chlorideto-iodide ratio in this well plots to the right of water from most 

wells in the Deep aquifer and could be a three-component 

mixture of brine, seawater, and native Deep aquifer water. The 

water in well 15L5 has the most similarity in composition to 

high-chloride brines from partly consolidated deposits that 

surround and underlie coastal aquifers in California (Izbicki, 

1996; Izbicki and others, 2003). Consistent with major-ion 

data and data from well 19Q3, water from partly consolidated 

marine rock may be the primary source for elevated iodide in 

well 4S/2W-15L5.

Geochemical Indicators of Groundwater 

Movement

The major-ion and chloride-to-iodide data suggest that 

recently recharged water is the primary source of groundwater 

to wells in the upper aquifer system. Water recharged at 

Quarry Lakes primarily affects the uppermost and adjacent 

wells. Sources of recharge to other upper aquifer system wells 

include recharge through local rivers and streams. Majorion composition changes caused by interactions with aquifer 

material as groundwater moves away from recharge sources, 

and laterally through the Deep aquifer, are evident in data 

for wells in the northern part of the Niles Cone groundwater 

subbasin. The major-ion and chloride-to-iodide data for 

water from Deep aquifer wells adjacent to Quarry Lakes is 

characteristic of groundwater intruded by seawater, indicating 

that water recharged at Quarry Lakes is not a major source 

of recharge to the Deep aquifer. The major-ion and chlorideto-iodide data for water from well 4S/2W-15L5 is similar 

to groundwater mixing with water from partly consolidated 

sediments underlying freshwater aquifers of the East Bay 

Plain groundwater subbasin, suggesting that water from partly 

consolidated marine rock may be an important source of 

chloride in the western part of the Niles Cone groundwater 

subbasin.

Noble-Gas and Tritium Analysis

Dissolved noble gases measured as part of this study 

include helium (He), neon (Ne), argon (Ar), and krypton (Kr). 

The inert nature of these gases, coupled with their differences 

in solubility at different temperatures, makes them useful 

for studying groundwater chronology, paleoclimatology, and 

mechanisms of groundwater recharge. The solubility of the 

noble gases in groundwater can be estimated by Henry’s law, 

as a function of the temperature and salinity of the water, 

and the atmospheric partial pressure of the gas (Ozima and 

Podosek, 1983). The total concentration of a gas in a sample 

is the sum of the equilibrium concentration and the excess 

air, radiogenic, and terrigenic components. Three models are 

commonly used to interpret dissolved gas concentrations in 

groundwater: (1) unfractionated air (UA) model (Heaton and 

Vogel, 1981), (2) partial reequilibration (PR) model (Stute and 

others, 1995), and (3) closed system equilibrium (CE) model 

(Aeschbach-Hertig and others, 2000). The UA model assumes 

the excess air component is atmospheric air resulting from 

complete dissolution of entrapped air bubbles. The PR model 

assumes elemental fractionation in the excess air component 

(lighter gases depleted relative to heavier gases) resulting from 

complete bubble dissolution followed by diffusive degassing. 

The CE model assumes that fractionation of excess air results 

from incomplete dissolution of entrapped air bubbles, and the 

fractionation factor is related to the individual gas solubilities. 

Neon oversaturation (positive ΔNe) has been used as a proxy 

for excess air and contamination during sample collection 

(Kipfer and others, 2002). Since Ne is not produced in the 

subsurface, any Ne in excess of that expected from solubility 

equilibrium is attributed to excess-air entrainment during 

recharge (ΔNe% = [(Nemeasured/Neeq.) –1] * 100) (Mazor, 

1972). Large quantities of excess air reflect rapid recharge 

from focused recharge during floods (or managed aquifer 

recharge), resulting in the dissolution of trapped air bubbles 

by increased water pressure. Dissolution and reequilibration 

processes were evaluated using the program NOBLEGAS 

(Aeschbach-Hertig and others, 1999) and determined not 

to effect excess-air concentrations in groundwater samples 

from the study area. An iterative subtraction approach was 

used to calculate the amount of excess air in a sample and 

estimate groundwater temperature at the time of recharge 

(Stute, 1989; Stute and others, 1995). This approach uses 

temperature as the fit target and varies the parameter values 

for excess air and reequilibration, while keeping the values 

for salinity and atmospheric pressure constant, such that 

the spread of the temperatures calculated for each noble gas 

is minimized. The measured noble gas concentrations are 

corrected for excess air, and a temperature is calculated using 

the corrected noble gas concentration. This process is repeated 

until agreement between the temperatures for each gas reach 

a desired agreement. In this study, groundwater recharge 

temperatures (NGT) were estimated from neon, argon, and 

krypton concentrations in groundwater. Helium was not used 

to calculate NGT because the measured He concentrations are 

significantly in excess of anticipated air-equilibration values.

The magnitude of the excess air component and NGT 

can be used as a proxy for relative infiltration conditions, as 

periods of recharge may be seasonal, and periods of greater 

recharge may result in the entrainment of larger amounts of 

excess air in groundwater (Heaton and Vogel, 1981; Heaton 

and others, 1986; Kulongoski and others, 2003). For the 

purpose of this study, groundwater NGT cooler than about 

11 oC and excess-air concentrations greater than 10 cubic 

centimeters per kilogram (cm3/kg) are interpreted to be 

consistent with focused recharge from winter stormflows that 

infiltrated rapidly through the unsaturated zone (entrapping 

air). In contrast, groundwater NGT warmer than 11 °C and 

excess-air concentrations lower than 10 cm3/kg are consistent 

with recharge from sustained streamflows along losing 

stream reaches downstream from the mountain front, with 

areal recharge from precipitation, or irrigation return flows 

that infiltrated slowly through the unsaturated zone prior to 

recharge (Stute and Schlosser, 2000).
24 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

The noble gas concentrations measured in groundwater 

from the Niles Cone and southern East Bay Plain groundwater 

subbasins are presented in appendix 6, along with salinity, 

ΔNe, the calculated NGTs, helium-4 ages, tritium, and 

tritium/3He ages. The observed excess-air component, ΔNe, 

ranges from 22.2 to 126.1 percent (appendix 6). The median 

ΔNe values for the upper aquifer system and the Deep aquifer 

were 94.9 and 56.6 percent, respectively. Although the 

medians suggest that the excess air component is greater in the 

upper aquifer system than in the Deep aquifer, this difference 

was not significant (P-value = 0.06). Values of NGTs in both 

the upper aquifer system and Deep aquifer range from near 

the average winter temperature of 11 °C to slightly greater 

than the average summer temperature of 18 °C. The median 

NGT of 15.4 °C was close to the average annual temperature 

of the area of 15 °C. Calculated NGTs derived from samples 

from wells in the upper aquifer system ranged from 10.6 ± 0.7 

to 19.2 ± 0.8 °C (fig. 12 and appendix 6). Calculated NGTs 

derived from samples from wells in the Deep aquifer ranged 

from 10.1 ± 0.7 to 18.1 ± 0.8 °C. 

Differences in excess air values and NGTs in upper 

aquifer system wells and Deep aquifer wells in the 

southeastern part of the study area suggest that recharge 

processes were different before the introduction of managed 

aquifer recharge. Presently, the Deep aquifer wells near 

Quarry Lakes are recharged from the shallow aquifer; 

therefore, similar excess air and NGT values for the upper 

aquifer system and the Deep aquifer would be expected 

following propagation of managed aquifer recharge through 

the entire aquifer system. However, the range in NGTs was 

greatest in the upper aquifer system and the Deep aquifer 

wells near recharge areas adjacent to Quarry Lakes and along 

Alameda Creek. Historically, recharge may have occurred 

during seasonal flow in Alameda and Dry Creeks. Well 17M6, 

and also wells 12C1 and 2H1, has a slightly cooler NGT, 

and lower excess air value, than upper aquifer system well 

17M7 and likely represents water that was recharged during 

sustained winter streamflow in Dry Creek. Well 13P5 has a 

slightly warmer NGT, and lower excess air value, than upperaquifer-system well 13P7 and likely represents water that was 

recharged during summer streamflows in Alameda Creek. The 

data also suggest that water in wells 15L5 and 4R1 may have 

been recharged from a source similar to that of well 13P5. 

The relative increase in excess air from the Deep aquifer wells 

13P5 and 17M6 to their respective upper aquifer system wells 

13P6 and 13P7, and 17M7 (fig. 12), is likely a result of rapid 

fluctuation of the water table, and resulting bubble entrapment 

and dissolution, possibly associated with managed aquifer 

recharge or rapid groundwater recharge along the mountain 

front. The shallowest wells near the recharge areas (17M8 

and 13P4) have excess-air values less than the deeper wells in 

the area, suggesting that these wells may receive water that is 

diffusely recharged from precipitation or as water lost to the 

unsaturated zone surrounding the areas of managed aquifer 

recharge. 

Average winter air 

temperature 11 °C

Average summer air temperature 18 °C

0.600

0.700

0.500

0.400

0.300

0.200

Argon, in cubic centimeters per kilogram water

200 300 400 500

Neon, in micro-cubic centimeters per kilogram water

0.250

0.350

0.450

0.550

0.650

150 250 350 450

13P4 Upper aquifer system wells 

Deep aquifer wells

EXPLANATION

15L5

20L20

14D3

12K8 3L1

17M8 29L6

4E1 4F3

17M6

12C1 2H1

10E4 13P5 4E1

13P4

13P7 13P6

4R1 15L5

17M7

Excess air, in cubic centimeters per kilogram

Water-air equilibrium line

Recharge temperature,

in degrees Celsius

0

5

10

15

0

5

10

15

20

25

Figure 12. Selected noble-gas concentrations in water from selected wells in the Niles Cone and southern East Bay Plain groundwater 

subbasins, Alameda County, California, 2002–03.
Geochemistry 25

The excess-air values and NGTs for wells in the transition 

zone and the southern East Bay Plain groundwater subbasin 

suggest areal recharge from precipitation. Most of the wells 

in the transition zone (10E4, 3L1, 4F3, and 4E1) have excessair values less than those of wells near Dry Creek and NGTs 

near the average annual temperature of 15 °C. Wells located 

north of the transition zone, in the southern East Bay Plain 

groundwater subbasin (29L6 and 20L20), have low excessair values and NGTs near the average annual temperature of 

15 °C. The NGTs for wells 29L6 and 20L20 were warmer than 

those estimated for groundwater recharged from San Lorenzo 

and San Leandro Creeks in the southern East Bay Plain 

groundwater subbasin to the north of the study area (Izbicki 

and others, 2003), suggesting that recharge in the area south of 

San Lorenzo Creek is from areal recharge from precipitation.

Tritium and Helium

Tritium (3H) was used to indicate the presence of recent 

(post-1950s) water. Tritium is a naturally occurring radioactive 

isotope of hydrogen that has a half-life of 12.43 years. In this 

study, tritium concentrations are reported in tritium units (TU); 

1 tritium unit is equivalent to 1 tritium atom in 1018 atoms 

of hydrogen (Taylor and Roether, 1982). Prior to 1952, the 

tritium concentration in precipitation in coastal California was 

about 2 TU. About 800 kilograms (kg) of tritium was released 

to the atmosphere as a result of the atmospheric testing of 

nuclear weapons during 1952–62 (Michel, 1976), and the 

tritium concentration of precipitation increased to a maximum 

of about 1,200 TU. After the cessation of atmospheric testing 

of nuclear weapons in 1962, the tritium concentration of 

precipitation decreased and present-day tritium levels in 

precipitation are near the pre-1952 levels. Because tritium is 

part of the water molecule, tritium is not affected by reactions 

other than radioactive decay, and—neglecting the effects of 

dispersion—tritium is an excellent tracer of the movement of 

groundwater recharged less than 50 years before present.

Helium has two stable isotopes, helium-3 (3He) and 

helium-4 (4He). Most helium in the natural environment 

(atmospheric) is helium-4; 3He concentrations are orders of 

magnitude smaller than 4He concentrations. As with many 

isotopes, the ratio of 3He to the more abundant isotope 4He can 

be measured more precisely than can the absolute abundance 

of a single isotope, and 3He data are reported as delta helium-3 

(δ3He). Helium concentrations in groundwater originate from 

several sources; these sources must be accounted for in order 

to estimate tritium/helium-3 apparent ages.

Water in contact with the atmosphere contains gases, 

including helium, as a result of equilibrium (Henry’s law) 

partitioning between atmosphere and water. In groundwater, 

final solubility equilibration between water and air occurs 

as water reaches the water table. Concentrations of gasses in 

the groundwater are a function of recharge temperature. For 

example, 3He is naturally present in the atmosphere, and water 

at 10 oC in equilibrium with the atmosphere will have a 3He 

concentration of 63.7 cm3/kg at 10 oC (Solomon and Cook, 

2000).

Another source of gases to ground water is known 

as excess air (Heaton and Vogel, 1981; Busenberg and 

Plummer, 2000; Stute and Schlosser, 2000). Excess air is 

thought to result from dissolution of air bubbles entrained by 

a fluctuating water table or trapped near the water table by 

recharging water. Gases, including helium and neon, in excess 

air are assumed to be added to groundwater in the proportions 

in which they exist in the atmosphere (unfractionated air; 

Heaton and Vogel, 1981; Schlosser and others, 1989). 

Unlike helium, neon does not have significant subsurface 

sources, so 3He and 4He from excess air are assumed to 

be proportional to the neon from excess air. Excess air 

trapped during groundwater recharge will increase the 3He 

contribution from atmospheric sources. Cook and Solomon 

(1997) estimated that the sensitivity of tritium/helium-3 ages 

to excess air ranges from –5.0 years per cubic centimeter per 

kilogram (cm3/kg) of excess air for very young groundwater to 

–0.25 year per cm3/kg of excess air for groundwater recharged 

25 years before present. 

Helium is also added to groundwater from uraniumand thorium-series decay reactions in the Earth’s crust 

(radiogenic). Radiogenic 3He produced in the subsurface 

through the decay of lithium-6 is small and does not affect the 

tritium/helium-3 age in most groundwater systems (Solomon 

and Cook, 2000). Production of 4He is the result of the decay 

of elements in the uranium-thorium radioactive decay series, 

other than 6Li. The 3He/4He ratio of radiogenic helium in deep 

crustal material is about 3 × 10–8 (Mamyrin and Tolstikhin, 

1984).

Because the 3He term is small for most groundwater and 

the 4He from radioactive decay is usually small for young 

ground water, the radiogenic 3He and 4He terms are combined 

with the helium terms from mantle degassing. The ratio of 

3

He to 4He in mantle gases is between 1 × 10–5 and 1.4 × 10–5

(Torgersen and Clarke, 1987). 

Finally, 3He is produced by the radioactive decay of 

tritium (tritiogenic helium). Solomon and Cook (2000) 

published a simultaneous solution to the 3He and 4He massbalance equations that uses measured 4

He concentrations, 

δ3He values, and neon concentrations (to constrain recharge 

temperatures and excess-air values) to calculate the 

concentration of 3He from the radioactive decay of tritium. 

Ground-water ages are then calculated on the basis of the 

radioactive decay of tritium. 

Tritium-Helium-3 Ages

Tritium in water from sampled wells in the upper aquifer 

system and Deep aquifer ranged from 7.2 to 46.6 TU and from 

less than the reporting limit of 0.2 to 16.6 TU, respectively 

(table 6–1). Tritium was present in water from wells in the 

Deep aquifer near Quarry Lakes and Alameda Creek and 

concentration decreased with distance from the recharge 

area to values below the reporting level of 0.2 TU (fig. 13). 
26 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Detections of tritium in Deep aquifer wells near recharge 

areas suggest a primary contribution of water recharged at the 

surface. Groundwater samples from Deep aquifer wells to the 

northwest have tritium levels less than the reporting limit of 

0.2 TU and are considered “tritium dead.” These waters have 

been isolated from surface recharge for more than 50 years.

Tritium/helium-3 ages for groundwater range from 6 

to >50 years (appendix 6). The tritium/helium-3 ages reflect 

the age of young fractions of groundwater recharged in the 

last 60 years. Water from Deep aquifer wells has less tritium 

and higher concentrations of helium, providing evidence that 

these groundwater samples are older than water from the 

upper-aquifer-system wells (appendix 6). Combined with 

lower recharge temperatures, this suggests that the Deep 

aquifer was mostly recharged under cooler, natural conditions 

(managed aquifer recharge leads to high ΔNe), occurring more 

than 50 years before the sample analyses year (2002). In the 

study area, none of the noble gas and tritium samples showed 

substantial mixing of young and old waters. Rather, there was 

a clear areal delineation between wells containing modern 

and pre-modern waters. In monitoring well nests 17M6–8 and 

13P5–7, groundwater ages were younger at shallower depths 

and older at greater depths (appendix 6). 

Helium-4 Ages

A naturally occurring isotope of helium present within the 

Earth’s crust, 4He, was used to estimate time since recharge for 

groundwater that does not contain measurable tritium and is 

older than the range of tritium/helium-3 dating techniques. The 

4

He ages are calculated from the accumulation of produced 

radiogenic 4He in groundwater. Contributions to the 4He 

inventory include two components: in situ production within 

the aquifer and a deep crustal flux (J0). Assuming that the 

deep crustal flux may be quantified (or neglected), the former 

component has chronological significance for the groundwater 

age. Stute and others (1992) proposed an approach by which 

the different helium sources may be separated, enabling either 

groundwater ages or crustal helium fluxes to be estimated. The 

relationship between apparent (corrected) groundwater age 

(τcorr, in years) and deep crustal flux entering the aquifer (J0, 4

He in cm3•STP•cm–2•yr–1) is given by equation 1 (Stute and 

others, 1992):

Sac15-0557_fig 13

Creek

San Francisco

Bay

EXPLANATION

122°10'

37°

38'

37°

36'

37°

34'

37°

32'

122°05' 122°00'

DIABLO RANGE

MISSION FAULT

HAYWARD FAULT

Quarry Lakes

Regional Park

0 1 2 MILES

0 1 2 KILOMETERS

880

13P5

17M6

12K8

12C1

2H1

10E4

4R1 3L1

4F6 4E1

29L6

20L20

14D3

15L5

92

Fremont

Hayward

Alameda

Creek

Alameda

Old

84

Creek

Dry

Background image is the intellectual property of Esri and is used herein under license.

Copyright © 2014 Esri and its licensors. All rights reserved. Base modified from U.S.

Geological Survey digital data, various scales; Lambert Conformal Conic projection;

North American Datum of 1983

Tritium activity, 

 in tritium units

≤0.2

0.2–0.6

0.6–10

≥10

Transition zone (Luhdorff

 and Scalmanini Consulting

 Engineers, 2003)

Faults

Roads

Figure 13. Spatial distribution of tritium concentrations in groundwater from selected Deep aquifer wells in the Niles cone and 

southern East Bay Plain groundwater subbasins, Alameda County, California, 2002–03.
Geochemistry 27

τ

φ ρ

corr

ex

o w

sol

He

J

z

He









 





4

0 4 (1)

where 4

Heex is the excess 4He (above concentrations 

expected from air equilibration and air 

bubble contamination),

φ is the effective porosity of the aquifer,

z0 is the depth (m) at which the deep crustal flux 

enters the aquifer, and

ρw is the density of water (~1 g/cm3). 

The 4He solution or accumulation rate (4Hesol in 

cm3•STP•g–1 H2O• yr–1) is given by equation 2, which 

combines the radioelement content of the aquifer {in brackets} 

with its physical properties (Andrews and Lee, 1979):

4 13 14 1 19 10 2 88 10 1 He U Th sol              ρ φ

φ

 . . (2)

where 

[U] and [Th] are the uranium and thorium concentrations in 

the aquifer rock in parts per million (ppm),

ρ is the bulk density of the aquifer rock (g/cm3),

Ʌ is the fraction of helium produced in the rock 

that is released into the water, assumed to 

be unity, and

	 φ is the fractional effective porosity of the 

aquifer rock.

Assuming aquifer properties for the Deep aquifer of 

porosity (φ) of 35 percent, and bulk density (ρ) of 1.76 g/cm3, 

with average uranium and thorium concentrations of 1.4 and 

5.2 milligrams per kilogram of alluvium (ppm; appendix 3), 

then the groundwater accumulation rate for 4He in the study 

area would be ~ 1.04 x 10–12 cm3•STP•g–1 H2O• yr–1, which 

yields 4He groundwater ages uncorrected for crustal He flux 

ranging from 0.0007 to >3.8 million years (Myr; eq. 2). 

These ages are many orders of magnitude greater than ages 

determined by 14C (see “Carbon-14 and Carbon-13” section). 

These results imply the presence of a significant deep crustal 

contribution of helium to the study area. Adopting a crustal 

flux (J0) of 3 × 10–6 cm3•STP•cm–2•yr–1 provides the best 

agreement between 4He and 14C ages and yields 4He ages 

between <1 to >11,000 years (appendix 6).

The distribution of 4He ages for Deep aquifer wells 

plotted on a map of the study area is presented in figure 14. 

Apparent 4He-derived ages are significantly younger for 

wells located near Quarry Lakes, with ages between <1 to 

26 years, whereas the ages of groundwater in wells to the 

west/northwest are greater, as much as >11,000 years. The old 

apparent 4He-derived ages for wells 15L5 and 14D3 could be 

influenced by a pocket of old water in the areas surrounding 

those wells. 

Isotopic Composition of Groundwater

Oxygen-18 and Deuterium

The proportion of the heavy stable isotopes of oxygen 

(18O) and hydrogen (2H, deuterium) in water molecules can 

be used to infer the source and evaporative history of water. 

Atoms of oxygen-18 (18O) and deuterium (2H) have more 

neutrons and a greater atomic mass than do atoms of the more 

common isotopes, oxygen-16 and hydrogen. The difference 

in weight results in differences in the physical and chemical 

behavior of the heavier, less abundant isotopes. 

Oxygen-18 and deuterium abundances are expressed 

as ratios of the heavy isotope to the light isotope, in delta 

notation (δ), as per mil (parts per thousand) differences, 

relative to Vienna Standard Mean Ocean Water (VSMOW; 

Gonfiantini, 1978). By convention, the value of both 

oxygen-18 and deuterium abundance ratios in VSMOW is 

0 per mil. Oxygen-18 (δ18O) and deuterium (δD) ratios relative 

to VSMOW can be measured more precisely than absolute 

abundances, and these ratios are useful in hydrologic studies 

(International Atomic Energy Agency, 1981). Based on 

duplicate analyses presented elsewhere (Coplen, 1994; Izbicki, 

1996), we have assumed a similar analytical precision of 

±0.05 per mil for δ18O and ±1.5 per mil for δD for the results 

presented here. 

The δ18O and δD composition of a water sample can 

provide a record of the source and evaporative history of 

the water, and differences in isotopic composition can be 

used to trace the water as it moves through the aquifer. Most 

precipitation originates from the evaporation of seawater, 

resulting in a linear correlation of δ18O and δD (fig. 15) that 

plots along a line known as the global meteoric water line 

(GMWL; Craig, 1961). Deviations from the GMWL are 

caused by differences in isotopic composition of precipitation 

if water vapor originated from evaporation of cooler or 

warmer water, and heavier isotopes are preferentially removed 

by precipitation as moist air masses move across continents. 

At a given location, the isotopic composition of precipitation 

trends to be an average value and is ultimately determined 

by local differences in the temperature of condensation 

and evaporative sources. Water that condensed at cooler 

temperatures (associated with higher altitudes, cooler climatic 

regimes, or higher latitudes) is lighter (more negative δ values) 

than water that condensed at warmer temperatures (associated 

with lower altitudes, warmer climatic regimes, and lower 

latitudes). Also, water that has been partially evaporated 

becomes enriched in heavier isotopes relative to its original 

composition and plots to the right of the GMWL, along an 

evaporative-trend line.
28 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Because of the temporal and spatial variability of δ18O 

and δD, and because precipitation is often not representative of 

groundwater, owing to runoff and recharge processes, shallow 

groundwater samples often are collected to characterize the 

stable isotopic composition of recharge (Kendall and Coplen, 

2001). Izbicki and others (2003) defined a local groundwater 

meteoric line by characterizing the stable isotopic composition 

of groundwater in the southern East Bay Plain groundwater 

subbasin. This local groundwater line is shown in figure 15

and is useful for discussing the evaporative history of 

groundwater sampled during this study.

Sources of recharge in the study area include diffuse 

infiltration from precipitation, infiltration from stream 

channels, and water artificially infiltrated at Quarry Lakes and 

behind seasonally inflated rubber dams in parts of Alameda 

Creek. Precipitation collected at a station near Quarry Lakes 

had δ18O and δD values of –7.7 and –45.8, respectively; for 

reasons stated in the “Methods” section, this single sample is 

not representative of annually weighted values (fig. 15). Some 

runoff in the Alameda Creek watershed is stored at reservoirs 

upstream from the study area where it may fractionate during 

evaporation before release downstream. Water in ACWD 

recharge ponds has a variable stable isotopic composition 

because it is derived from both local runoff in the Alameda 

Creek basin and water imported from the Sacramento–San 

Joaquin River Delta. Water imported from the Sacramento–

San Joaquin River Delta may be mixed with local runoff 

stored in reservoirs in the Alameda Creek watershed or may be 

discharged directly to a tributary of Alameda Creek upstream 

from the study area. Water imported from the South Bay 

Aqueduct has a δ18O value of –9 to –10 per mil (Moran and 

Halliwell, 2004). Imported water deliveries began in the early 

1960s partly to dilute effluent from wastewater treatment 

plants that was discharged to streams in the Alameda Creek 

watershed (Lopp, 1981). Although most wastewater has 

been exported via pipeline to the San Francisco Bay since 

1980, the stable isotopic composition of groundwater near 

Alameda Creek that was recharged before 1980 may be partly 

influenced by wastewater. The δ18O and δD composition 

of the wastewater has not been characterized. During late 

summer, much of the water in Alameda Creek is derived 

from groundwater originating from Quarry Lakes. The stable 

isotopic composition of water in the recharge ponds (δ18O = 

–5.71; δD = –48), sampled in December 1997 (Moran and 

Halliwell, 2004), indicates that recharge water infiltrating 

from the ponds was evaporated (fig. 15). The relative volume 

of imported water and local Alameda Creek sources used for 

managed aquifer recharge at the ACWD recharge ponds varies 

considerably from year to year. 

SAC15-0557_fig 14

San Francisco

Bay

Creek

Quarry Lakes

Regional Park

DIABLO RANGE

MISSION FAULT

HAYWARD FAULT

92

880

13P5

17M6

12K8

12C1

14D3

10E4

2H1

3L1 4R1

4F6

4E1

29L6

20L20

15L5

Fremont

Hayward

84

Alameda Old

Alameda

Creek

Creek

Dry

EXPLANATION

Helium ages, in years

 before present

Transition zone (Luhdorff

 and Scalmanini Consulting

 Engineers, 2003)

Faults

Roads

<1,000

1,000–<5,000

5,000–<10,000

≥10,000

0 1 2 MILES

0 1 2 KILOMETERS

122°10'

37°

38'

37°

36'

37°

34'

37°

32'

122°05' 122°00'

Background image is the intellectual property of Esri and is used herein under license.

Copyright © 2014 Esri and its licensors. All rights reserved. Base modified from U.S.

Geological Survey digital data, various scales; Lambert Conformal Conic projection;

North American Datum of 1983

Figure 14. Spatial distribution of 4He ages from selected wells in the Niles Cone and southern East Bay Plain groundwater subbasins, 

Alameda County, California, 2002–03.
Geochemistry 29

The δ18O and δD composition of water from sampled 

wells in the study area ranged from –5.4 to –7.3 per mil and 

–42.5 to –50.5 per mil, respectively (table 5–1). The range in 

δ18O and δD values is small given the many sources of water 

having different isotopic compositions. Water from wells in 

the upper aquifer system and the Deep aquifer near Alameda 

Creek and Quarry Lakes (4S/2W-13P4–7 and 4S/1W-17M6–8) 

shows signs of evaporation and plot along an evaporation 

trend line (fig. 15). The evaporative signal apparent from 

wells near (within 2 miles) the Quarry Lakes recharge ponds 

is likely a result of isotopically depleted water (less negative 

values) recharging from the ponds. Wells screened in the upper 

aquifer system show heavier isotopic ratios, and plot further 

right along the evaporative trend line, than the Deep aquifer 

wells because of mixing of the managed recharge source with 

other water farther from the source. Most samples plot slightly 

below the meteoric water line along the local groundwater line 

of Izbicki and others (2003). Isotopic data from wells 20L20 

and 19Q3 suggest that groundwater in the southern East 

Bay Plain groundwater subbasin is derived from a different 

source, likely areal recharge. The isotopic composition of 

water in well 4S/2W-2H1 has a δD value greater than the 

other Deep aquifer wells in the Niles Cone subbasin and 

is similar to local precipitation measured at USGS site 

373425121582101, indicating that the source of water in this 

well is predominantly infiltration of precipitation.

−90

0

−9 0

Evaporative

trend line 

19Q3

Seawater

mixing line 

Meteoric

mixing line 

Meteoric

mixing line 

Local groundwater line

Evaporative

trend line 

SAC15-0557_fig 15ab

−80

−70

−60

−50

−40

−30

−20

−10

−8 −7 −6 −5 −4 −3 −1

Deuterium/protium ratio

Oxygen-18/oxygen-16 ratio

Oxygen-18/oxygen-16 ratio

−58

−56

−54

−52

−50

−48

−46

−44

−8.0 −7.0 −6.0

Deuterium/protium ratio

−2

−42

−40

−5.0

EXPLANATION

Seawater

Quarry Lakes Regional Park recharge

 ponds (Moran and Halliwell, 2004)

13P6

15L5

Local precipitation measured at Alameda County

 Water District rooftop (USGS 373425121582101)

 on November 8, 2002

Well sampled by Izbicki and others, 2003

Upper aquifer system wells

Deep aquifer wells

15L5

2H1

20L20

13P5

17M6 13P6

13P7

17M7

13P4

17M8

12K10

Carbon-14 and Carbon-13

Carbon-14 (14C) is a naturally occurring radioactive 

isotope of carbon having a half-life of 5,730 years (Manov 

and Curtiss, 1951). Carbon-14 is formed in the atmosphere by 

the interaction of cosmogenic radiation with nitrogen (Clark 

and Fritz, 1997). Atmospheric carbon-14 is present as carbon 

dioxide (CO2), which can then be incorporated into various 

hydrospheric (oceans, lakes, and groundwater) and biospheric 

(plants and animals) reservoirs. Whether through infiltration 

of water or the decay and release of biomass into the soil zone, 

once these intermediate sources of carbon are isolated from 

the atmosphere, the carbon-14 content in the dissolved carbon 

steadily decreases.

Carbon-14 that has been isolated from the atmosphere is 

seldom only affected by radioactive decay. Chemical reactions 

can dilute carbon-14 by either the addition of dissolved 

inorganic carbon (DIC) that lacks carbon-14 or by the removal 

of DIC that contains carbon-14 (Clark and Fritz, 1997). 

Carbon-14 concentrations can be decreased when carbon is 

added to groundwater by the dissolution of calcite or dolomite, 

which are devoid of carbon-14 and are often said to contain 

“dead” carbon (Freeze and Cherry, 1979). The addition of 

DIC from these sources dilutes the original carbon-14 content 

to give the appearance of older water, as does the production 

of DIC from oxidation of organic matter that is devoid of 

carbon-14. Above ground nuclear testing increased the amount 

of carbon-14 in the atmosphere, similar to tritium, within the 

last 50 years. Groundwater recharged within this period likely 

contains 14C above natural background concentrations of 

100 pmC. 

Figure 15. Relations of delta oxgen-18 (δ18O) with delta deuterium (δD) in water from wells, Niles Cone and southern East Bay Plain 

groundwater subbasins, Alameda County, California, 2002–03.
30 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Because of its long half-life, carbon-14 can be used 

to estimate groundwater ages ranging from 1,000 to less 

than 30,000 years before present (Clark and Fritz, 1997). 

Radiocarbon dating is based on measuring the loss of the 

parent radionuclide carbon-14 in a given sample, assuming 

the initial carbon-14 concentration is known and that losses 

or gains of carbon-14 are minimal or can be quantified (Clark 

and Fritz, 1997). The activity of carbon-14 in a sample is 

reported in percent modern carbon, which indicates the 

carbon-14 activity of the sample relative to that of modern 

carbon, defined as 95 percent of the carbon-14 activity of the 

National Bureau of Standards oxalic acid in 1950 (Clark and 

Fritz, 1997). 

Ratios of the stable isotopes carbon-13 to the far more 

abundant carbon-12 (delta carbon-13, δ13C) were used in this 

study as indicators of biogeochemical and carbon-exchange 

processes that can affect estimates of carbon-14 ages. Because 

carbonate minerals and DIC exchange carbon isotopes 

(equilibration), groundwater can acquire a less negative 

delta δ13C value as it moves through the aquifer. Values of 

δ13C can also be affected by decomposition (oxidation or 

mineralization) of organic matter buried in the aquifer because 

organic material has a more negative δ13C composition 

than does inorganic carbon so that carbon isotopes would 

become lighter. Values of δ13C were used to make qualitative 

inferences about the extent to which these processes have 

caused the carbon-14 age to overestimate the actual time 

elapsed since recharge in this study. 

Carbon-14 activities in DIC in the Deep aquifer ranged 

from 16 to 86 pmC and had a median of 50 pmC (table 5–1). 

These carbon-14 activities correspond to uncorrected ages 

ranging from 1,300 to 15,000 years before present (ybp), with 

a median uncorrected age of 5,700 ybp. Dissolved inorganic 

carbon delta carbon-13 values ranged from –13.3 to –15.3 per 

mil. Carbon-13 values became lighter with increasing distance 

along the groundwater flowpath, north from Quarry Lakes. 

Additionally, δ13C measured in water from wells within the 

Niles Cone groundwater subbasin (table 5–1) are generally 

less negative than in water from wells within the southern East 

Bay Plain groundwater subbasin (represented by wells 20L20 

and 29L6), including wells sampled by Izbicki and others 

(2003).

Interpretation of Carbon-14 Data

The computer program NETPATH (Plummer and others, 

1991) was used to account for reactions that affect DIC and 

adjust the measured carbon-14 activities to estimate the 

age (time since recharge) of groundwater along a flowpath 

extending from recharge areas along Alameda Creek near 

Quarry Lakes, through the transition zone within the Deep 

aquifer, into the East Bay Plain groundwater subbasin 

(flowpath B–B′; fig. 4). Restriction of groundwater flow near 

the transition zone that was not discernible from water-level 

data can be detected using groundwater ages of water from 

wells across the area (Izbicki and Martin, 1997). 

Inputs to NETPATH model calculations include changes 

in groundwater chemistry and isotopic composition along the 

study flowpath (fig. 16; appendix 7) and aquifer mineralogy 

(table 3–1). Chemical data are used to calculate saturation 

indexes (SI; fig. 16) that indicate if a mineral will tend to 

dissolve if present in the aquifer (negative values) or, in the 

absence of thermodynamic constraints, precipitate (positive 

values) from groundwater onto aquifer materials. Large 

magnitude values (either positive or negative) may indicate 

the presence of constraints on these processes. For example, 

primary minerals such as albite or mica cannot precipitate in 

comparatively low-temperature/low-pressure groundwater 

environments; similarly, there may be kinetic constraints on 

clay-mineral formation that limit their precipitation from 

groundwater. Chemical data and the mass-balance of the 

various elements in groundwater and minerals also constrain 

NETPATH model calculations representing the dissolution and 

precipitation and the mass-transfer of dissolved constituents 

along the flowpath (Plummer and others, 1991). The carbon-13 

composition of organic material in the aquifer was assumed 

to be –25 per mil, consistent with carbon from a mixture of 

plants having C3 and C4 photosynthetic pathways and similar 

to the value used in NETPATH calculations used to estimate 

groundwater age in the East Bay Plain groundwater subbasin 

(Izbicki and others, 2003).

For the purpose of model calculations, carbon-14 activity 

(Ao) of groundwater at the beginning of the flowpath through 

the aquifer was estimated using an approach described by 

Verhagen and others (1991; fig. 17). This approach, based on 

field data, is applicable in systems where groundwater may 

contain modern groundwater recharged after the atmospheric 

testing of nuclear weapons beginning in the early 1950s. 

Carbon-14 data are shown in rank order, expressed as percent 

greater than or equal to, from largest to smallest. Carbon-14 

activities generally exceeded 69.37 pmC in water samples 

from wells containing tritium. This value was selected as the 

initial carbon activity, Ao, for modeling purposes and was 

also used to calculate uncorrected carbon-14 ages from the 

measured percent modern carbon values. Water from three 

wells having lower carbon-14 activities contain measurable 

tritium, suggesting that the water from these wells (1) is a 

mixture of modern water containing tritium and older water 

that does not contain tritium or (2) chemical reactions have 

occurred in water from these wells that has resulted in the 

addition of carbon from aquifer materials that does not contain 

carbon-14, resulting in a lower than expected carbon-14 

activity. Water from one of these wells, 12C1 near Dry Creek, 

has comparatively high tritium activity of 7.8 TU, and the 

water likely contains a high fraction of modern groundwater. 

Water from well 14D3 near Alameda Creek has a tritium 

activity of 0.4 TU, indicating a smaller but measurable 

fraction of modern groundwater. Tritium also was detected 

in water from well 20L20 at an activity of 0.6 TU near the 

downgradient end of the study flowpath, suggesting a small 

amount of modern water consistent with recent recharge in 

that area. Carbon-14 ages for these wells were not adjusted 

for the presence of modern water, and actual ages of the older 

groundwater in these wells are likely older than the ages 

calculated by NETPATH.
Geochemistry 31

sac15-0557_fig 16abc

35,000

35,000

Concentration, in millimoles

−4

−8

−6

−4

−3

−2

−2

−1

0

0

1

2

3

4

2

4

6

8

35,000

Cumulative mass transfer, in millimoles Saturation index

30,000 25,000 20,000 15,000 10,000 5,000 0

Under-saturated

30,000 25,000 20,000 15,000 10,000 5,000 0

30,000 25,000 20,000 15,000 10,000 5,000 0

Over-saturated pH

−1.0

−0.5

0.5

Cation exchange, in millimoles

0.0

1.0

29L6 4E1 4F3 3L1 12C1

B (Northwest) B’ (Southeast) Direction of groundwater flow

5 0

1

2

3

4

5

6

7

6

7

8

9 A

B

C

12K8

Distance along flow path, in feet

Distance along flow path, in feet

Distance along flow path, in feet

EXPLANATION

EXPLANATION

EXPLANATION

Ca2+ SO4

2- Mg Na+ 2+ Cl− HCO3- pH

Calcite (CaCO3) Albite Gypsum Mica Montmorillonite Anorthite Kaolinite

Ca/Na Exchange Silicate Carbonate Clay Carbon H2

S Gypsum

Figure 16. Selected changes in chemical and isotopic composition of water from wells used to interpret carbon-14 data along section 

B–B’, Niles Cone and southern East Bay Plain groundwater subbasins, Alameda County, California, 2002–03.
32 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Major-ion composition of groundwater along flowpath 

B–B′ gradually changes from a mixed composition to a more 

sodium-type water downgradient (fig. 10), consistent with 

cation exchange previously identified as important reactions 

in the East Bay Plain groundwater subbasin (Izbicki and 

others, 2003). The largest changes in major-ion composition, 

accompanied by increases in pH, occur between wells 4F3 and 

4E1 near the downgradient end of the transition zone between 

the Niles Cone and East Bay Plain groundwater subbasins 

within the Deep aquifer. NETPATH calculations provide 

estimates of (1) saturation indices for selected minerals at 

each well along the flowpath, (2) mass transfer of major 

cations and anions, and (3) cation exchange between each 

well. Positive mass transfer values indicate that the constituent 

is increasing in concentration, and negative values indicate 

that the constituent is decreasing in concentration. Positive 

cation exchange values indicate that calcium is exchanging 

for sodium on clay minerals, and negative values indicate 

that sodium is exchanging for calcium on clay minerals. The 

NETPATH calculations indicate saturation of groundwater 

with respect to calcite and exchange of sodium for calcium on 

clay minerals along flowpath B–B′ (fig. 16). Because calcium 

is a divalent cation, it is preferentially absorbed by exchange 

sites on clay minerals; however, in environments where the 

equilibrium is shifted to an oversaturation of sodium, such as 

aquifers influenced by seawater intrusion, sodium ions may 

replace calcium ions on exchange sites (Izbicki, 1991). 

NETPATH calculations also indicate consumption of 

organic carbon within the aquifer, likely through biological 

processes. Consistent with consumption of organic carbon 

from aquifer materials by microbiological processes, alkalinity 

increases and δ13C values become increasingly negative 

with distance downgradient along flowpath B–B′ (fig. 16). 

Measured and model-calculated δ13C values generally agree 

within 0.5 per mil.

sac15-0557_fig 16de

35,000

35,000 30,000 25,000 20,000 15,000 10,000 5,000 0

30,000 25,000 20,000 15,000 10,000 5,000 0

29L6 4E1 4F3 3L1 12C1

B (Northwest) B’ (Southeast) Direction of groundwater flow

D

E

−16

−15

−14

−13

−12

12K8

Carbon-13/carbon-12 ratio, in per mil

0

2,000

4,000

6,000

8,000

10,000

Age, in years before present

Distance along flow path, in feet

Distance along flow path, in feet

EXPLANATION

EXPLANATION

Measured carbon-13 Calculated carbon-13

Uncorrected carbon-14 ages Corrected carbon-14 ages

Figure 16. —Continued
Geochemistry 33

Field data and NETPATH results show a decrease 

in carbon-14 activity with distance downgradient along 

flowpath B–B′ (fig. 16). Uncorrected carbon-14 ages range 

from near modern near the recharge areas to as much as 

9,000 years before present (ybp) downgradient. Interpreted 

carbon-14 ages are slightly less, ranging from modern 

to about 7,340 ybp (table 7–1). The difference between 

uncorrected and interpreted ages results from addition of 

carbon that does not contain carbon-14 from microbiological 

respiration of organic carbon within aquifer materials along 

the flowpath. Both uncorrected and interpreted ages indicate 

large changes in groundwater age near the downgradient 

end of the transition zone, whereas stable water isotope data 

(δ18O and δD; fig. 15) suggest the source of groundwater 

recharge in this area is relatively unchanged. The slight 

decrease in groundwater age in water from well 4E1 to 29L6 

suggests that well 29L6 is not at the end of the B–B′ flowpath. 

Uncorrected carbon-14 age data from well 20L20 suggest 

that groundwater age increases from north to south in the 

East Bay Plain groundwater subbasin and that flowpaths may 

be converging at the transition zone between the Niles Cone 

and the East Bay Plain groundwater subbasins. Groundwater 

velocities calculated from interpreted carbon-14 ages range 

from 3 to 12 ft/yr in the Deep aquifer of the Niles Cone 

groundwater subbasin and decrease to as little as 0.5 ft/yr 

near the transition to the southern East Bay Plain groundwater 

subbasin. Groundwater flow rates within the Deep aquifer, 

calculated on the basis of groundwater 14C ages and distance 

along the flowpath, decrease by an order of magnitude 

from 11.6 ft/yr between wells 4S/2W-3L1 and 4S/2W-4F3 

to 0.5 ft/yr between wells 4S/2W-4F3 and 4S/2W-4E1 just 

south of the southern East Bay Plain groundwater subbasin 

transition zone boundary (table 7–1). These results are 

consistent with lithologic changes (Luhdorff and Scalmanini 

Consulting Engineers, 2003) within the transition zone that 

separates the two groundwater subbasins and acts to limit 

flow between the Niles Cone and southern East Bay Plain 

groundwater subbasins. Because the converging flowpaths and 

lithologic changes at the transition zone restrict movement of 

groundwater from the Niles Cone groundwater subbasin into 

the East Bay Plain groundwater subbasin, water recharged 

at the Quarry Lakes likely remains within the Niles Cone 

groundwater subbasin.

Limitations of Carbon-14 Interpretations

Carbon-14 ages calculated using NETPATH are 

interpretive and subject to uncertainty. For aquifers for which 

the chemistry is well understood, interpreted carbon-14 ages 

are within ±20 percent of the actual value (Davis and Bentley, 

1982). In areas where present-day recharge may not reflect the 

composition of recharge for older groundwater, the greatest 

source of uncertainty in interpreting carbon-14 data is in 

determining the initial chemistry, carbon-14 activity, and δ13C 

composition of the recharge water. 

In this study, the carbon-14 age calculated for water 

from well 12C1, which is a mixture of modern and older 

groundwater (samples with tritium detections greater than or 

equal to 0.8 TU and carbon-14 activities less than or equal to 

95 pmC), is an average age. The age of the older fraction of 

groundwater composing this mixture was not calculated. It is 

likely that the age of the older fraction of water is greater than 

the age shown in table 7–1 and on figure 16.

SAC15-0557_fig 17

0

20

40

60

80

100

120

Carbon-14 activity, in percent modern carbon

0 10 20 30 40 50 60 70 80 90 100

Percent greater than or equal to

EXPLANATION

Tritium activity greater than

 0.2 tritium units

Tritium activity less than

 0.2 tritium units

Figure 17. Plot of rank order carbon-14 data, expressed as cumulative exceedance percentage, in water from sampled wells in the 

Niles Cone and southern East Bay Plain groundwater subbasins, Alameda County, California, 2002–03. Tritium concentrations are shown 

using filled and open circle symbols.
34 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Summary

The principal water-bearing units in the Niles Cone and 

southern East Bay Plain groundwater subbasins are located 

west of the Hayward Fault. The aquifers (from shallowest 

to deepest) are the Newark, Centerville, Fremont, and Deep 

aquifers; these were originally defined in the Niles Cone 

groundwater subbasin and projected to the southern East 

Bay Plain groundwater subbasin. The Newark, Centerville, 

and Fremont aquifers are thickest and most continuous in 

the Niles Cone groundwater subbasin. Unlike the Niles 

Cone groundwater subbasin to the south, alluvial fans in 

the southern East Bay Plain groundwater subbasin were not 

deposited by large streams, and as a result, sediments in 

shallow aquifers are finer grained and more discontinuous 

than in the Niles Cone groundwater subbasin. Fine-grained 

sediments deposited between the alluvial fans of the Niles 

Cone and southern East Bay Plain groundwater subbasins 

interrupt lateral continuity of coarse-grained layers and may 

restrict interbasin flow of groundwater.

Beginning in 1974, ACWD imported water to supplement 

natural recharge to the aquifer system in the Niles Cone 

groundwater subbasin by recharging water through ponds 

at Quarry Lakes Regional Park. This recharged water was 

intended to increase hydraulic heads in the area and halt 

intrusion of water from San Francisco Bay into the aquifer 

systems, and along with other projects in the area, to improve 

groundwater quality. Although water levels in wells in the 

region increased, the effect of managed aquifer recharge 

was not otherwise quantified. Hydrologic, InSAR, and 

geochemical data for 2002 and 2003 were collected and 

analyzed to evaluate the geologic and hydrologic controls on 

groundwater movement through aquifers between the Niles 

Cone and southern East Bay Plain groundwater subbasins on 

the east side of San Francisco Bay, California, in cooperation 

with the East Bay Municipal Utility District, City of Hayward, 

and Alameda County Water District.

Groundwater in the upper aquifer system and Deep 

aquifer flows to the west and north from recharge areas near 

Quarry Lakes and along Alameda Creek. Water levels were 

about 20 ft lower in the Deep aquifer than in the upper aquifer 

system. Water levels in the Deep aquifer were as much as 9 ft 

below sea level during this study. Steep water-level gradients 

to the south of the recharge areas are likely the result of 

pumping at the Mowry well field and Aquifer Reclamation 

Program (ARP) wells. To the north, fewer wells completed 

solely in the upper aquifer system were available to measure 

water levels because of the finer-grained nature of the aquifer 

deposits in this area. Water-level data show groundwater 

in the Deep aquifer flows to the north toward the southern 

East Bay Plain groundwater subbasin. Changes in the slope 

of the water-level contours near the transition zone between 

the Niles Cone and southern East Bay Plain groundwater 

subbasins are consistent with changes in lithology, or could 

indicate structural features such as faults or folds, that restrict 

groundwater flow.

Water recharged at Quarry Lakes affects the hydraulic 

heads in nearby wells in which both the upper aquifer system 

and Deep aquifer respond rapidly and with little lag between 

recharge and the measured responses to recharge (fig. 5). 

InSAR data show land surface deformation in response 

to aquifer recharge of about 0.8 in. (20 mm). Measured 

deformation is greater to the west and northwest (fig. 6), 

downgradient from groundwater recharge areas where 

aquifers are finer-grained and elastic, and less near recharge 

areas where aquifers are coarser-grained. The extent of the 

uplift shown on interferograms may not represent the extent 

of the movement of water from managed aquifer recharge, 

but instead results from a pressure response. InSAR data 

also show land surface deformation in response to pumping, 

suggesting land surface deformation is elastic and occurs 

rapidly.

Streamflow data show that during the period of the study, 

the section of Alameda Creek nearest Quarry Lakes was a 

losing section, and the reach of Alameda Creek as much as 

1.5 miles (fig. 3) upstream from the tidally affected section 

was a gaining reach. Water from the losing reach of Alameda 

Creek likely recharges the upper aquifer system and the Deep 

aquifer. Large streamflows during winter months could cause 

losing conditions along the entire nontidally affected reach of 

Alameda Creek. Under predevelopment conditions, sustained 

flow in Alameda Creek may have been great enough to 

provide a consistent source of recharge to the local aquifers.

Groundwater in the study area was fresh, with dissolved 

solids concentrations in sampled wells less than 1,080 mg/L. 

Values of pH were near neutral to alkaline, with increasing 

pH with depth and distance from groundwater recharge areas. 

Water from sampled wells in the upper aquifer system had 

varied dissolved oxygen concentrations ranging from oxic 

(2.9 mg/L) to reduced (<0.2 mg/L). Water from sampled wells 

in the Deep aquifer was generally reducing. Water from upperaquifer-system wells located near Quarry Lakes is marked by 

higher calcium and magnesium percentages than water from 

most wells in the Deep aquifer, indicating influence by water 

recharged at Quarry Lakes and from the ponded areas behind 

the inflatable dams in Alameda Creek. The effect of past 

intrusion of water from San Francisco Bay and high-chloride 

water from partly consolidated marine rock underlying the 

study area can be seen in water from some wells in the Deep 

aquifer that have chloride concentrations as high as 350 mg/L. 

Water from some Deep aquifer wells has elevated chloride 

concentrations and major-ion concentrations indicative of 

exchange of sodium for calcium and magnesium on clay in 

aquifer deposits. Water from well 4S/2W-15L5 has major-ion 

proportions suggesting the source of high-chloride water to 

well 15L5 is likely from partly consolidated marine rock.
References Cited 35

Groundwater recharge temperatures estimated using 

noble-gas data ranged from 10.1 ± 0.7 to 19.2 ± 0.8 oC, 

warmer than those estimated for focused recharge along San 

Lorenzo and San Leandro Creeks in the southern East Bay 

Plain groundwater subbasin, north of the study area (Izbicki 

and others, 2003). The warmer recharge temperatures in 

the study area may reflect year-round recharge from Quarry 

Lakes and Alameda Creek rather than winter recharge from 

infiltration of winter stormflows in the smaller, unmanaged 

streams that recharge the East Bay Plain groundwater 

subbasin. The δ18O and δD data in shallow wells near the 

recharge area indicate evaporative modification of water stored 

in the recharge ponds, or behind the rubber dams, prior to 

infiltration. In contrast, isotopic data from a few wells suggest 

that groundwater in the southern East Bay Plain groundwater 

subbasin is derived from a different source, likely areal 

recharge or infiltration of precipitation.

Tritium/helium-3 age data show that upper aquifer 

system and Deep aquifer wells near Quarry Lakes contain 

water that has been recently recharged. Tritium/helium-3 ages 

for groundwater range from 6 to 50 years for these wells and 

were greater than 50 years for the rest of the wells in the study 

area. Tritium/helium-3 ages and tritium activities decreased 

away from Quarry Lakes with distance from the recharge area 

to values below the reporting level. Although 4He ages and 

uncorrected 14C ages differed, generally they both increased 

downgradient.

NETPATH analyses of water-chemistry data show that 

as water flows through the aquifer systems, concentrations of 

sodium (plus potassium relative to calcium plus magnesium) 

increase owing to primary silicate weathering and (or) 

exchange of calcium and magnesium for sodium on clay 

within aquifer deposits (Izbicki and others, 1992; Izbicki 

and others 2003). Carbon-14 groundwater ages in the 

Deep aquifer, corrected for reactions that occur between 

groundwater and aquifer materials, range from 830 to 

7,340 years before present. Ages increase northward along 

the flowpath from the Niles Cone groundwater subbasin 

toward the southern East Bay Plain groundwater subbasin, 

with large changes in groundwater age within the transition 

zone separating the Niles Cone from the southern East 

Bay Plain groundwater subbasins. Groundwater flow rates 

within the Deep aquifer decrease by an order of magnitude 

from 11.6 ft/yr between wells 4S/2W-3L1 and 4S/2W-4F3 to 

0.5 ft/yr between wells 4S/2W-4F3 and 4S/2W-4E1 just south 

of the southern East Bay Plain groundwater subbasin transition 

zone boundary. These results are consistent with restricted 

groundwater flow between the two groundwater subbasins 

and consistent with the result of lithologic changes within the 

transition zone and converging groundwater flowpaths north 

of the transition zone. Additionally, converging groundwater 

flowpaths north of the transition zone from different recharge 

areas within the two subbasins may restrict transfer of water 

between the two subbasins. As a consequence, water recharged 

at Quarry Lakes directly affects water levels and water quality 

in wells in the vicinity of the recharge facility, and that water 

likely remains within the subbasin.

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Appendix 1 41

Appendix 1. Location and Construction Data and Water-Level Measurements Collected by the U.S. Geological Survey During 2002 for Wells Drilled in the Niles Cone and Southern East Bay Plain Groundwater SubbasinsTable 1–1. Location and construction data and water-level measurements collected by the U.S. Geological Survey during fall 2002 for wells drilled in the Niles Cone and southern East Bay Plain groundwater subbasins, Alameda County, California. [Water-level data shown in bold are used in figures 3 and 4. Abbreviations: bls, below land surface; bmsl, below mean sea level; F, flowing; ft, foot; mm/dd/yyyy, month/day/year; NAVD 88, North American Vertical Datum of 1988; USGS, U.S. Geological Survey; *, mean sea level is 6.75 ft above the station datum for Station 9414750, Alameda, Calif., of 3.56 ft (NAVD 88); —, no data; >, greater than]

State 

well 

number

USGS 

identification 

number

Well 

type

Primary 

aquifer 

contributing 

water 

to well

Land-surface 

altitude, 

NAVD 88 

(ft)

 Depth to 

upper-most 

perforation 

interval 

(ft)

Depth to 

bottom-most 

perforation 

interval 

(ft)

Well 

depth 

(ft bls)

Depth 

to 

water 

(ft bls)

Waterlevel 

altitude 

NAVD 88 

(ft)

Date of 

water-level 

measurement

(mm/dd/yyyy)

Waterlevel 

(ft bmsl)*

Upper aquifer system

4S/1W-17M7 373457122002102 Observation Centerville-Fremont 52.7 215 255 260 42.4 10.3 03/19/2002 0.04S/1W-17M7 373457122002102 Observation Centerville-Fremont 52.7 215 255 260 47.2 5.5 10/28/2002 –4.84S/1W-17M8 373457122002103 Observation Newark 52.4 80 120 125 28.6 23.8 03/22/2002 13.54S/1W-17M8 373457122002103 Observation Newark 52.4 80 120 125 35.5 16.9 10/28/2002 6.64S/1W-18R1 373313122002401 Observation Newark 51.1 — — 150 28.7 22.4 04/16/2002 12.14S/1W-19E2 373418122011901 Observation Newark 40.6 — — 147 19.9 20.7 05/01/2002 10.44S/1W-19J6 373409122003601 Observation Newark 53.1 — — 145 31.0 22.2 05/01/2002 11.84S/1W-19N14 373349122011803 Observation Newark 43.1 — — 100 23.2 19.9 05/06/2002 9.64S/1W-20H3 373422121592201 Observation Newark 70.2 — — 65 40.8 29.4 04/16/2002 19.14S/1W-20J6 373404121591901 Observation Newark 61.8 — — 80 33.4 28.4 05/06/2002 18.14S/1W-20R1 373356121593302 Observation Newark 61.9 — — 85 38.2 23.7 06/06/2002 13.44S/1W-28D12 373348121590401 Observation Newark 65.6 — — 160 48.9 16.7 05/03/2002 6.44S/1W-29A6 373345121591701 Observation Newark 63.9 — — 127 42.9 21.0 05/03/2002 10.74S/1W-29C7 373543121595901 Observation Newark 58.0 — — 61 37.0 21.0 05/06/2002 10.74S/1W-29C8 373345121595101 Observation Newark 60.1 — — 59 38.9 21.3 05/06/2002 10.94S/1W-30A5 373341122003703 Observation Newark 54.9 — — 150 34.8 20.1 05/02/2002 9.84S/1W-30E4 373329122011802 Observation Newark 44.2 — — 155 25.6 18.6 05/02/2002 8.34S/2W-12K9 373545122015002 Observation Fremont 56.1 300 310 310 56.1 0.0 11/05/2002 –10.34S/2W-12K10 373545122015003 Observation Centerville 56.1 210 240 240 54.8 1.3 11/05/2002 –9.04S/2W-12K11 373545122015004 Observation Newark 56.4 110 150 150 40.5 15.9 11/05/2002 5.6

Appendix 1
42 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins State well number USGS identification number Well type Primary aquifer contributing water to well Land-surface altitude, NAVD 88 (ft) Depth to upper-most perforation interval (ft) Depth to bottom-most perforation interval (ft) Well depth (ft bls) Depth to water (ft bls) Water- level altitude NAVD 88 (ft) Date of water-level measurement (mm/dd/yyyy) Water- level (ft bmsl)* Upper aquifer system—Continued 4S/2W-13E3 373514122022101 Observation Newark 30.6

—

— 144 12.3 18.3 04/25/2002 8.0

4S/2W-13P4 373447122021904 Observation Newark 28.6 48 78 145 9.2 19.4 03/27/2002 9.14S/2W-13P4 373447122021904 Observation Newark 28.6 48 78 145 13.6 15.0 10/28/2002 4.74S/2W-13P6 373447122021902 Observation Fremont 28.9 340 360 360 19.6 9.3 03/26/2002 –1.04S/2W-13P6 373447122021902 Observation Fremont 28.9 340 360 360 26.0 2.9 10/28/2002 –7.44S/2W-13P7 373447122021903 Observation Centerville 28.7 190 280 280 19.0 9.8 03/26/2002 –0.64S/2W-13P7 373447122021903 Observation Centerville 28.7 190 280 280 25.4 3.4 10/28/2002 –7.04S/2W-14D5 373521122033103 Observation Fremont 16.7 260 280 280 16.5 0.3 11/06/2002 –10.14S/2W-14D6 373521122033104 Observation Centerville 16.9 180 220 220 16.5 0.4 11/06/2002 –9.94S/2W-14D7 373521122033105 Observation Newark 16.8 70 110 110 5.1 11.7 11/06/2002 1.44S/2W-14H3 373517122024301 Observation Newark 27.7

—

— 125 10.4 17.3 05/02/2002 7.0

4S/2W-14L6 373507122031901 Observation Newark 17.6

—

— 120 3.4 14.2 04/17/2002 3.9

4S/2W-14R3 373441122024101 Observation Newark 28.6

—

— 110 11.1 17.5 04/16/2002 7.2

4S/2W-23J2 373403122024501 Observation Newark 26.8

—

— 122 9.2 17.6 05/06/2002 7.3

4S/2W-24F11 373421122021301 Observation Newark 31.9

—

— 70 12.9 19.0 04/16/2002 8.7

4S/2W-25D3 373343122022602 Observation Newark 25.7

—

— 154 8.1 17.6 04/26/2002 7.3

4S/2W-26K6 373321122025002 Observation Newark 22.5

—

— 145 7.3 15.2 05/01/2002 4.9

Deep aquifer

3S/2W-20L20 373912122065001 Public production Deep 49.8 500 585 600 36.4 13.4 03/07/2002 3.13S/2W-29L6 373832122064801 Public production Deep 43.0 480 580 600 42.4 0.6 10/30/2002 –9.83S/2W-32D2 373759122064901 Observation Deep 23.8

—

— 550 29.5 –5.7 11/08/2002 –16.0

3S/2W-35J11 373733122025901 Observation Deep 16.0

—

— 580 20.5 –4.5 11/13/2002 –14.8

4S/1W-7P4 373543122010101 Observation Deep 69.2

—

— 476 69.3 –0.1 11/13/2002 –10.4

4S/1W-17M6 373457122002101 Observation Deep 52.6 420 460 460 46.1 6.5 03/19/2002 –3.84S/1W-17M6 373457122002101 Observation Deep 52.6 420 460 460 50.5 2.1 10/28/2002 –8.24S/1W-28D1 373348121590503 Observation Deep 65.7

—

— 445 67.0 –1.3 11/08/2002 –11.6

Table 1–1. Location and construction data and water-level measurements collected by the U.S. Geological Survey during fall 2002 for wells drilled in the Niles Cone and southern East Bay Plain groundwater subbasins, Alameda County, California. Water—Continued[Water-level data shown in bold are used in figures 3 and 4. Abbreviations: bls, below land surface; bmsl, below mean sea level; F, flowing; ft, foot; mm/dd/yyyy, month/day/year; NAVD 88, North American Vertical Datum of 1988; USGS, U.S. Geological Survey; *, mean sea level is 6.75 ft above the station datum for Station 9414750, Alameda, Calif., of 3.56 ft (NAVD 88); —, no data; >, greater than]
Appendix 1 43

State 

well 

number

USGS 

identification 

number

Well 

type

Primary 

aquifer 

contributing 

water 

to well

Land-surface 

altitude, 

NAVD 88 

(ft)

 Depth to 

upper-most 

perforation 

interval 

(ft)

Depth to 

bottom-most 

perforation 

interval 

(ft)

Well 

depth 

(ft bls)

Depth 

to 

water 

(ft bls)

Waterlevel 

altitude 

NAVD 88 

(ft)

Date of 

water-level 

measurement

(mm/dd/yyyy)

Waterlevel 

(ft bmsl)*

Deep aquifer—Continued

4S/1W-30A2 373341122003701 Observation Deep 54.5 — — 400 54.9 –0.4 11/08/2002 –10.74S/1W-30E3 373329122011801 Observation Deep 44.8 — — 593 45.0 –0.2 11/08/2002 –10.54S/2W-2H1 373648122023601 Private production Deep 39.0 429 459 472 34.4 4.6 03/20/2002 –5.74S/2W-3L1 373646122042701 Private production Deep 13.5 367 442 452 22.6 –9.1 11/07/2002 –19.44S/2W-4E1 373708122055101 Public production Deep 12.4 470 525 535 10.5 1.9 03/07/2002 –8.44S/2W-4F3 373702122052201 Observation Deep 12.7 440 525 550 9.8 3.0 03/21/2002 –7.44S/2W-4F6 373700122052301 Public production Deep 13.0 358 524 534 8.8 4.2 03/07/2002 –6.14S/2W-4R1 373638122045901 Public production Deep 12.5 370 456 466 14.9 –2.4 10/29/2002 –12.74S/2W-10E4 373601122042901 Observation Deep 17.2 400 440 440 18.6 –1.4 11/04/2002 –11.74S/2W-12C1 373620122015901 Public production Deep 68.9 410 487 512 64.1 4.8 03/20/2002 –5.54S/2W-12K8 373545122015001 Observation Deep 55.8 470 510 510 56.7 –0.9 11/05/2002 –11.24S/2W-13P5 373447122021901 Observation Deep 28.7 400 420 420 20.7 8.1 03/26/2002 –2.34S/2W-13P5 373447122021901 Observation Deep 28.7 400 420 420 27.3 1.5 10/28/2002 –8.94S/2W-14D3 373521122033101 Observation Deep 16.7 400 450 450 18.9 –2.2 11/06/2002 –12.54S/2W-14D4 373521122033102 Observation Deep 16.6 520 540 540 18.1 –1.5 11/06/2002 –11.84S/2W-15L5 373457122041001 Observation Deep 10.3 430 470 470 11.7 –1.4 10/29/2002 –11.74S/2W-25D1 373343122022601 Observation Deep 24.9 — — 517 24.9 0.0 11/13/2002 –10.34S/2W-26K4 373321122024901 Observation Deep 23.0 — — 501 22.6 0.4 11/13/2002 –9.9

Table 1–1. Location and construction data and water-level measurements collected by the U.S. Geological Survey during fall 2002 for wells drilled in the Niles Cone and southern East Bay Plain groundwater subbasins, Alameda County, California. —Continued[Water-level data shown in bold are used in figures 3 and 4. Abbreviations: bls, below land surface; bmsl, below mean sea level; F, flowing; ft, foot; mm/dd/yyyy, month/day/year; NAVD 88, North American Vertical Datum of 1988; USGS, U.S. Geological Survey; *, mean sea level is 6.75 ft above the station datum for Station 9414750, Alameda, Calif., of 3.56 ft (NAVD 88); —, no data; >, greater than]
44 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins
Appendix 2 45

Appendix 2. U.S. Geological Survey National Water-Quality Laboratory 

Analytical Methods and Reporting Levels for Analysis of Groundwater and 

Surface-Water Samples

Fishman, M.J., ed., 1993, Methods of analysis by the 

U.S. Geological Survey National Water Quality 

Laboratory—Determination of inorganic and organic 

constituents in water and fluvial sediments: U.S. Geological 

Survey Open-File Report 93–125, 217 p., available at 

https://pubs.er.usgs.gov/publication/ofr93125.

Fishman, M.J., ed., and Friedman, L.C., 1989, Methods for 

determination of inorganic substances in water and fluvial 

sediments: U.S. Geological Survey Techniques of WaterResources Investigations 05–A1, 545 p., available at 

https://pubs.er.usgs.gov/publication/twri05A1.

Gleason, J.D., Friedman, Irving, and Hanshaw, B.B., 1969, 

Extraction of dissolved carbonate species from natural 

water for carbon-isotope analysis: U.S. Geological Survey 

Professional Paper 650–D, p. D248–D250, available at 

https://pubs.er.usgs.gov/publication/pp650D.

Jones, S.R., Garbarino, J.R., 1999, Methods of analysis 

by U.S. Geological Survey National Water Quality 

Laboratory—Determination of arsenic and selenium in 

water and sediment by graphite furnace atomic adsorption 

spectrometry: U.S. Geological Survey Open-File 

Report 98–639, 39 p., available at 

https://pubs.er.usgs.gov/publication/ofr98639.

Patton, C.J., and Truitt, E.P., 1992, Methods of analysis 

by the U.S. Geological Survey National Water Quality 

Laboratory—Determination of total phosphorus by a 

Kjedahl digestion method and an automated colorimetric 

finish that include dialysis: U.S. Geological Survey OpenFile Report 92–146, 39 p., available at 

https://pubs.er.usgs.gov/publication/ofr92146.

Struzeski, T.M., DeGiacomo, W.J., and Zayhowski, E.J., 1996, 

Methods of analysis by the U.S. Geological Survey National 

Water Quality Laboratory—Determination of dissolved 

aluminum and boron in water by inductively coupled 

plasma-atomic emission spectrometry: U.S. Geological 

Survey Open-File Report 96–149, 17 p., available at 

https://pubs.er.usgs.gov/publication/ofr96149.

Thatcher, L.L., Janzer, V.J., and Edwards, K.W., 1977, 

Methods for determination of radioactive substances 

in water and fluvial sediments: U.S. Geological Survey 

Techniques of Water-Resources Investigations 05–A5, 95 p., 

available at https://pubs.er.usgs.gov/publication/twri05A5.

Samples were collected by the U.S. Geological 

Survey during 2002–03. Samples from domestic and public 

production wells were collected using existing pumping 

systems; samples from unused wells and monitoring wells 

were collected using a small diameter, stainless steel, 

submersible pump (Wilde, 1999a). The surface-water sample 

from Dry Creek was collected using the pump-sampling 

method described in Wilde (1999a).

Field parameters (pH, specific conductance, temperature, 

and alkalinity) were measured for each sample collected 

by the U.S. Geological Survey as described in Wilde 

(1999a). Dissolved oxygen was measured in the field by 

the U.S. Geological Survey using colorimetric methods 

(CHEMets Kit K-7512 or K7501). Selected samples were 

processed in the field and sent to the U.S. Geological Survey’s 

National Water-Quality Laboratory (NWQL) for inorganic 

analysis. Samples for inorganic analysis of dissolved 

constituents were filtered in the field using a capsule filter 

having a pore size of 0.45 mm (Wilde, 1999b). Nutrients 

were preserved by chilling at 4 oC and were analyzed within 

seven days. Trace elements were preserved by acidification 

to pH <2.0. Stable isotope samples were sent to the USGS 

Reston Stable Isotope Laboratory. Carbon isotope samples 

were sent to the University of Waterloo Environmental Isotope 

Laboratory. Dissolved gas samples and tritium samples 

were sent to the University of Rochester Rare Gas Facility. 

Analytical methods and associated reporting limits are listed 

in table 2–1.

References Cited

Beukens, R.P., 1992, Radiocarbon accelerator mass 

spectrometry—Background, precision and accuracy, in

Taylor, R.E., Long, Austin, and Kra, R.S., eds., Radiocarbon 

after four decades: New York, Springer-Verlag, p. 230–239, 

accessed April 4, 2012, at 

https://doi.org/10.1007/978-1-4757-4249-7_16.

Coplen, T.B., Wildman, J.D., and Chen, Julie, 1991, 

Improvements in the gaseous hydrogen-water equilibration 

technique for hydrogen isotope-ratio analysis: Analytical 

Chemistry, v. 63, no. 9, p. 910–912, accessed April 4, 2012, 

at https://doi.org/10.1021/ac00009a014.

Epstein, S., and Mayeda, T., 1953, Variation of O18 content of 

waters from natural sources: Geochimica et Cosmochimica 

Acta, v. 4, no. 5, p. 213–224, accessed May 16, 2012, at 

https://doi.org/10.1016/0016-7037(53)90051-9.

Appendix 2
46 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Table 2–1. U.S. Geological Survey National Water-Quality Laboratory analytical methods and reporting levels for analysis of 

groundwater samples.

[ASF, automated-segmented flow; mg/L, milligram per liter; pCi/L, picocurie per mil; std, standard; oC, degrees Celsius; μS/cm, microsiemen per centimeter at 

25 oC; μg/L, microgram per liter]

Constituent Methodology Reporting 

limit Reference

Field parameters

pH pH electrode 0.1 std units Fishman and Friedman, 1989

Specific conductance Wheatstone bridge 1.0 μS/cm Fishman and Friedman, 1989

Alkalinity Titrimetry with sulfuric acid 1.0 mg/L Fishman and Friedman, 1989

Dissolved oxygen Colorimetric indigo-carmine 0.006 mg/L White and others, 1990

Major ions

Calcium, dissolved Inductively coupled plasma 0.011 mg/L Fishman, 1993

Chloride, dissolved Ion chromatography 0.08 mg/L Fishman and Friedman, 1989

Dissolved solids Gravimetric, residue on evaporation at 180 oC 10.0 mg/L Fishman and Friedman, 1989

Magnesium, dissolved Inductively coupled plasma 0.008 mg/L Fishman, 1993

Potassium, dissolved Atomic adsorption, flame 0.09 mg/L Fishman and Friedman, 1989

Silica, dissolved Colorimetry, ASF 0.48 mg/L Fishman and Friedman, 1989

Sodium, dissolved Inductively coupled plasma 0.06 mg/L Fishman, 1993

Sulfate, dissolved Ion chromatography 0.11 mg/L Fishman and Friedman, 1989

Nutrients

Nitrite, dissolved Colorimetry, ASF, 0.006 mg/L Fishman, 1993

Nitrite + nitrate, dissolved Colorimetry, ASF, cadmium reduction-diazotization 0.047 mg/L Fishman, 1993

Ammonia, dissolved Colorimetry, ASF, salicylate-hypochlorite 0.041 mg/L Fishman, 1993

Ammonia + organic nitrogen, dissolved Colorimetry, ASF, microkjeldahl digestion 0.10 mg/L Patton and Truitt, 1992

Phosphorus, dissolved Colorimetry, ASF, microkjeldahl digestion 0.05 mg/L Patton and Truitt, 1992

Orthophosphate, dissolved Colorimetry, ASF, phosphomolybdate 0.018 mg/L Fishman, 1993

Trace elements

Arsenic, dissolved Graphite furnace atomic adsorption 2.0 μg/L Jones and Garbarino, 1999

Barium, dissolved Inductively coupled plasma 0.9 μg/L Fishman, 1993

Boron, dissolved Inductively coupled plasma 13.0 μg/L Struzeski and others, 1996

Bromide, dissolved Colorimetry, ASF 0.01 mg/L Fishman and Friedman, 1989

Fluoride, dissolved ASF, ion-selective electrode 0.16 mg/L Fishman and Friedman, 1989

Iodide, dissolved Colorimetry, ASF, ceric-arseneous 0.001 mg/L Fishman and Friedman, 1989

Iron, dissolved Inductively coupled plasma 10.0 μg/L Fishman, 1993

Manganese, dissolved Inductively coupled plasma 3.2 μg/L Fishman, 1993

Isotopes

Carbon-14 Accelerator mass spectrometry 0.3 percent Beukens, R.P., 1992

Carbon-13/carbon-12 Mass spectrometry 0.15 per mil Gleason and others, 1969

Deuterium/protium Mass spectrometry 2.0 per mil Coplen and others, 1991

Oxygen-18/oxygen-16 Mass spectrometry 0.2 per mil Epstein and Mayeda, 1953

Tritium Electrolytic enrichment and liquid scintillation 1.0 pCi/L Thatcher and others, 1977

White, A.F., Peterson, M.L., and Soibau, R.D., 1990, 

Measurement and interpretation of low levels of dissolved 

oxygen in ground water: Ground Water, v. 28, p. 584–590.

Wilde, F.D., ed., 1999a, Collection of water samples: 

U.S. Geological Survey Techniques of Water-Resources 

Investigations, book 9, chap. A4, 231 p., accessed 

November 2002 at https://water.usgs.gov/owq/FieldManual/

chapter4/pdf/Archive/chapter4.pdf.

Wilde, F.D., ed., Radtke, D.B., Gibs, Jacob, and Iwatsubo, 

R.T., 1999b, Processing of water samples: U.S. Geological 

Survey Techniques of Water-Resources Investigations, 

book 9, chap. A5, with sections 5.6.1.F, 5.6.4.A, and 

5.6.4.B, 233 p., accessed November 2002 at 

https://water.usgs.gov/owq/FieldManual/chapter5/html/

Ch5_contents.html.
Appendix 3 47

Appendix 3. Aquifer Mineralogy, Niles Cone Groundwater Subbasin, Alameda 

County, California

(fig. 3–1), suggesting that this may be an important reaction 

between groundwater and aquifer materials. On the basis of 

scanning electron microscopy with spectral analysis, small 

amounts of chlorite were present in aquifer deposits. Highly 

soluble chloride minerals are not likely to be present within 

freshwater aquifers underlying the Niles Cone groundwater 

subbasin. Dissolution of chlorapatite, or recrystallization into 

the more common form apatite, may explain small increases 

in chloride concentrations that alter chloride-to-bromide 

and chloride-to-iodide ratios (fig. 11) as groundwater flows 

through aquifer deposits. These increases are not nearly as 

large as chloride concentrations measured in water from 

underlying aquifers or increases resulting from seawater 

intrusion.

References Cited

Amonette, J.E., and Zelazny, L.W., eds., 1994, Quantitative 

methods in soil mineralogy—Proceedings of a symposium 

sponsored by Division S-9 of the Soil Science Society of 

America, San Antonio, Texas, October 23–24, 1990: Soil 

Science Society of America, 452 p.

Izbicki, J.A, Borchers, J.W., Leighton, D.A., Kulongoski, J.T., 

Fields, Latoya, Galloway, D.L., and Michel, R.L., 2003, 

Hydrogeology and geochemistry of aquifers underlying 

the San Lorenzo and San Leandro areas of the East Bay 

Plain, Alameda County, California: U.S. Geological Survey 

Water-Resources Investigations Report 2002–4259, 71 p., 

available at https://pubs.er.usgs.gov/publication/wri024259.

Appendix 3

The elemental composition of cores and cuttings was 

determined by inductively coupled plasma–mass spectrometry 

(table 3–1; Briggs and Meier, 2002). The mineralogy 

of selected cores and cuttings was determined by X-ray 

diffraction (table 3–2; Amonette and Zelazny, 1994). Images 

of selected materials were obtained using a scanning electron 

microscope equipped with a spectral analyzer (Amonette and 

Zelazny, 1994). Mineralogic analyses were done on cuttings 

and core material from the Deep aquifer at a depth of 517 ft 

below land surface at well 14D3 and on a composite of 

coarse-grained outcrop material at Horseshoe Lake recharge 

pond (old gravel quarry) sampled from 2 ft and 20 ft below 

land surface, on the northwest shore (table 3–1). Mineralogic 

data were used as inputs to the computer program NETPATH 

for interpretation of carbon-14 data discussed in this report. 

Analysis of the uranium (U) and thorium (Th) content of 

coarse-grained sediments in both the Deep aquifer and surface 

deposits were used as a basis for estimating the magnitude of 

in situ generation of He and He isotopic composition.

Results are similar to previous analyses of core material 

from the East Bay Plain groundwater subbasin (Izbicki and 

others, 2003) in that quartz is the dominant mineral and a 

smaller amount of feldspar minerals are present. Primary and 

secondary minerals are listed in table 3–1. Scanning electron 

microscope images show little evidence of weathering or 

dissolution of mineral grains in cores and cuttings (fig. 3–1). 

Grain morphology and spectral analysis suggest that the bulk 

of the aquifer is composed of relatively nonreactive quartz. 

This is consistent with X-ray diffraction data in table 3–1. 

Scanning electron microscope images collected as part of this 

study show evidence of secondary precipitation of calcite 

Northwest shore of Horseshoe Lake (Quarry 

Lakes) lithic fragment—quartz, potassium 

feldspar, albite

14D3 deep sand, overview—Q, quartz; A, albite; 

L, lithic fragment; K, potassium feldspar; M, mica

14D3 deep fines—calcite precipitation

Figure 3–1. Scanning electron microscopy (SEM) images of typical mineral grains from core material from selected sites in the Niles 

Cone groundwater subbasin, Alameda County, California [μm, micrometers].
48 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Table 3–1. Elemental composition of samples from Lake Chad well (4S/2W-14D3) at 517 feet deep and outcrop on northwest shore of 

Quarry Lakes, Niles Cone groundwater subbasin, Alameda County, California.

[ft, foot; kg, kiliogram; mg, milligram; NW, northwest; w/o, without; x, present; <, less than; ?, uncertain; —, not present]

Sample identifier 4S/2W-14D3 

(bulk)

NW 

Quarry Lakes 

composite

4S/2W-14D3 

(deep sand 

w/o fines)

4S/2W-14D3 

(deep fines)

Sample description Detection 

limit

Drilling mud 

impregnated core, 

517 ft deep

Outcrop—

sandy gravel 

near recharge ponds

Washed and 

sieved core, 

517 ft

Hydrometer fines—

native formation plus drilling 

mud from core, 517 ft deep

Elements (mg/kg)

Gold Ag 2 5.3 2.3 <2 <2

Arsenic As 1 5.8 6.7 1.8 4.7 

Barium Ba 0.2 398 502 295 549 

Beryllium Be 0.03 0.82 0.92 0.62 1.1 

Bismuth Bi 0.06 0.14 0.12 <0.06 0.13 

Calcium Ca 100 8,280 13,400 6,620 11,700 

Cadmium Cd 0.007 0.34 0.13 0.16 0.26 

Cerium Ce 0.1 28.9 39.9 22.7 47.4 

Cobalt Co 0.03 11.9 13.0 8.4 17.0 

Chromium Cr 0.5 135 158 98.2 196 

Ceasium Cs 0.003 1.6 2.0 1.0 2.8 

Copper Cu 2 22.3 25.7 41.2 65.9 

Iron Fe 50 27,200 31,500 18,700 41,200 

Gallium Ga 0.02 9.3 10.9 7.1 14.1 

Potassium K 20 8,810 11,100 7,540 14,400 

Lanthanum La 0.05 15.0 21.6 13.0 24.2 

Lithium Li 0.3 23.8 25.2 17.9 33.5 

Magnessium Mg 6 13,000 15,600 9,840 19,400 

Manganese Mn 0.7 403 608 293 511 

Molybdenum Mo 0.05 0.95 0.52 0.23 0.67 

Sodium Na 20 14,200 16,900 16,200 38,100 

Niobium Nb 0.1 4.5 6.6 3.2 9.4 

Nickel Ni 0.3 77.3 93.1 58.6 122 

Phosphorus P 5 543 566 538 27,000 

Lead Pb 0.4 8.74 20.0 4.21 10.8 

Rubidium Rb 0.01 34.6 43.5 27.3 56.2 

Antimony Sb 0.04 0.51 0.94 0.24 0.50 

Scandium Sc 0.04 9.5 11.9 6.6 14.2 

Strontium Sr 0.8 108 134 87.1 154 

Tantalum Ta 0.02 0.44 0.61 0.24 0.97 

Thorium Th 0.1 4.52 6.05 3.11 7.27 

Titanium Ti 40 2,450 3,210 1,990 3,120 

Thallium Tl 0.08 0.20 0.26 0.15 0.34 

Uranium U 0.02 1.30 1.48 1.01 1.98 

Vanadium V 0.2 72.4 90.0 47.0 110 

Tungsten W 0.1 2.4 1.3 0.8 1.4

Yttrium Y 0.05 14.4 16.4 14.2 21.5 

Zinc Zn 3 54.5 63.8 45.9 92.9 
Appendix 3. Aquifer Mineralogy, Niles Cone Groundwater Subbasin, Alameda County, California 49

Table 3–2. Mineralogical composition and optical observations of samples from Lake Chad well (4S/2W-14D3) at 517 feet deep and 

outcrop on northwest shore of Quarry Lakes, Niles Cone groundwater subbasin, Alameda County, California.

[ft, foot; kg, kiliogram; mg, milligram; NW, northwest; w/o, without; x, present; <, less than; ?, uncertain; —, not present]

Sample identifier 4S/2W-14D3 

(bulk)

NW 

Quarry Lakes 

composite

4S/2W-14D3 

(deep sand 

w/o fines)

4S/2W-14D3 

(deep fines)

Sample description Detection 

limit

Drilling mud 

impregnated core, 

517 ft deep

Outcrop—

sandy gravel 

near recharge ponds

Washed and 

sieved core, 

517 ft

Hydrometer fines—

native formation plus drilling 

mud from core, 517 ft deep

Minerals (percent abundance)

Quartz — 54.0 46.0 63.0 36.0 

Potassium feldspar — 3.0 — 7.0 6.0 

Chlorite — 5.0 4.0 2.0 5.0 

Muscovite — 4.0 8.0 4.0 12.0 

Kaolinite — <2 ? — —

Monmorillonite — ? <2? — —

Kao-mont mixed — 10.0 12 5.0 17.0 

Plagioclase feldspar — 23.0 27 19.0 23.0 

Hematite — ? ? — —

Calcite — — 1 — —

Optical observations — Gravel—rounded rock 

fragments with 

some clay and iron 

coatings; fine-grained 

material–quartz sand, 

sandstone fragments.

Gravel—rounded rock 

fragments with some 

large quartz and feldspar 

blocky fragments; finegrained material—rock 

fragments, quartz, clay 

coatings.

Angular to 

semi-rounded 

quartz.

Fine-grained quartz, large 

sheets of material.

Minerals from X-ray diffraction

Quartz — x x x x

Albite — x x x x

Kaolinite/montmorillonite — x x x x

Orthoclase, barian — — — x x

Orthoclase — x — — —

Clinochlore — x x x x

Muscovite — x x x x

Calcite — — — — —

Kaolinite — x ? — —

Montmorillonite — x x — —

Hematite — ? ? — —

Minerals from scanning electron microscope (major or minor component)

Organics — None None None None

Lithics — — Major — —

Quartz — Major Major Major Major

Albite — Major Minor Major —

Mica — Major — Major Minor

Sodium phosphate — — — — Major

Potassium feldspar — — — — Minor

Andalusite barite — Minor — — —

Ilmenite — Minor Minor Minor —

Iron oxide — Minor Minor Minor —

Rutile — Minor — — Minor

Apatite — Minor — — —

Clays — Minor Minor Minor —

Mica — Major Minor Major —

Calcite — — — — Minor

Anorthite — — Major — —
50 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins
Appendix 4 51

Appendix 4. Streamflow Data Collected by the U.S. Geological Survey during 

April 2002

Appendix 4

Table 4–1. Streamflow data collected by the U.S. Geological Survey during April 2002, Alameda Creek, California.

[ft3/s, cubic foot per second; N, North; W, West; °, degrees; ′, minutes; ′′, seconds; —, no data]

Site 

number 

(as shown 

in figure 3)

Distance 

downstream 

from site 1, 

in miles

April 24, 2002, 

morning

April 24, 2002, 

afternoon

April 25, 2002, 

midday

Discharge, 

in ft3/s

Gage 

height, 

in feet

Rating Discharge, 

in ft3/s

Gage 

height, 

in feet

Rating Discharge, 

in ft3/s

Gage 

height, 

in feet

Rating

Temperature, 

in degrees 

Celsius

1* 0 2.84 0.87 Good 0.48 0.78 Poor 0.41 0.72 Poor 19.0

2 0.4 2.94 0.68 Good 0.58 0.485 Fair — — — 20.5

3 0.8 — — — — — — 0 5.07 Estimated —

4 1.1 1.18 5.63 Fair — — — 0.01 5.39 Poor 21.5

5 1.3 1.16 — Good 0.42 7.325 Poor — — — 23.0

6 1.9 1.43 8.13 Poor 0.602 8.08 Fair 0.21 8.02 Poor 20.5

7 2.5 1.28 11.16 Fair 1.79 11.66 Fair — — — 22.5

8 3.0 2.86 12.39 Good — — — 1.9 12.31 Fair 22.5

9 3.6 3.61 — Good 3.96 — Good 3.37 — Good 21.0

*

Site 1 is located at 37°33′57.13052′′ N., 121°59′50.33553′′ W.
52 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins
Appendix 5 53

Appendix 5. Physical Property, Major-Ion, Trace-Element, and Isotopic Data for Groundwater, StreamWater, and Precipitation Samples Collected and Analyzed by the U.S. Geological Survey

Appendix 5

Table 5–1. Physical property, major-ion, selected trace-element, and isotopic data for groundwater, stream-water, and precipitation samples collected and analyzed by the U.S. Geological Survey, southern East Bay Plain and Niles Cone groundwater subbasins, Alameda County, California, 2002–03.[Data analyzed by U.S. Geological Survey (USGS). Location of sites shown in figure 1. Abbreviations: A, at; ACWD, Alameda County Water District; BLDG, building; CaCO3, calcium carbonate; E, approximate value; hhmm, 24-hour time format in hours and minutes; mg/L, milligram per liter; mm/dd/yyyy, month/day/year; N, nitrogen; PO4, phosphate; SiO2, silicon dioxide; °C, degrees Celsius; μg/L, microgram per liter; μS/cm, microsiemen per centimeter at 25 °C; <, actual value less than value shown; —, no data]

State

well 

number

Aquifer Local name USGS identification number Date (mm/dd/yyyy) Time (hhmm) Dissolved oxygen (mg/L) pH, field (standard units) pH, lab (standard units) Specific conduc- tance field (μS/cm) Specific conduc- tance lab (μS/cm) Tempera- ture water (°C)

4S/1W-17M7 Upper aquifer system Kraftile 373457122002102 03/19/2002 1450 2.4 7.1 7.6 861 882 17.84S/1W-17M8 Upper aquifer system Kraftile 373457122002103 03/22/2002 1000 0.3 6.9 7.3 708 718 174S/2W-12K10 Upper aquifer system Pacific 373545122015003 11/05/2002 1600 0.3 7.1 7.5 890 E862 18.44S/2W-13P4 Upper aquifer system Rowland Park 373447122021904 03/27/2002 1230 0.2 7 7.3 1,030 1,050 18.54S/2W-13P6 Upper aquifer system Rowland Park 373447122021902 03/26/2002 1300 1.9 7.2 7.6 1,280 1,290 18.34S/2W-13P7 Upper aquifer system Rowland Park 373447122021903 03/27/2002 1040 2.9 7.2 7.5 1,210 1,220 17.73S/2W-20L20 Deep aquifer Hayward D2 373912122065001 10/29/2002 1000 1 7.3 7.6 640 604 18.43S/2W-29L6 Deep aquifer MMWA 4 373832122064801 10/30/2002 1500 0.1 7.4 7.6 831 778 23.14S/1W-17M6 Deep aquifer Kraftile 373457122002101 03/19/2002 1130 0.2 7.4 7.7 945 956 18.74S/2W-2H1 Deep aquifer BART 373648122023601 03/20/2002 1620 0.1 7.6 7.8 680 683 22.34S/2W-3L1 Deep aquifer Danone 373646122042701 03/27/2002 1520 1 7.4 7.6 583 603 21.44S/2W-4E1 Deep aquifer Hayward E 373708122055101 10/30/2002 1130 0.1 7.5 7.8 896 E847 21.64S/2W-4F3 Deep aquifer City Yard B deep MW 373702122052201 03/21/2002 1100 0.2 7.2 7.6 651 665 21.64S/2W-4R1 Deep aquifer Hayward C 373638122045901 10/29/2002 1350 0.1 7.6 7.7 907 864 20.74S/2W-10E4 Deep aquifer Tidewater 373601122042901 11/04/2002 1330 0.1 7.6 7.9 798 E806 214S/2W-12C1 Deep aquifer Whipple 373620122015901 03/20/2002 1100 0.2 7.3 7.8 805 816 22.14S/2W-12K8 Deep aquifer Pacific 373545122015001 11/05/2002 1120 0.1 7.8 8 597 582 20.54S/2W-13P5 Deep aquifer Rowland Park 373447122021901 03/26/2002 1020 0.2 7.2 7.5 1,430 1,470 18.54S/2W-14D3 Deep aquifer Lake Chad 373521122033101 04/16/2003 1500 0.1 8.6 8.6 600 573 21.24S/2W-14D4 Deep aquifer Lake Chad 373521122033102 11/06/2002 1410 0.1 7.6 7.8 922 911 224S/2W-15L5 Deep aquifer Contempo Park 373457122041001 10/29/2002 1900 0.1 8 8 1,550 1,520 22.1Dry Creek near 

Union City

— — 373630122010501 04/17/2003 1000 10.5 8 8.1 599 578 11.9

USGS 

373425121582101 PRECIP SAMPLER ACWD ROOFTOP INFLATION BLDG A NILES

— — 373425121582101 11/08/2002 1000 — 6 — 12 — —
54 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins State well number Date (mm/dd/yyyy) Hardness, total (mg/L as CaCO3

)

Calcium, 

dissolved

(mg/L as Ca)

Magnesium, 

dissolved

(mg/L as Mg)

Potassium, 

dissolved

(mg/L as K)

Sodium, 

dissolved

(mg/L as Na)

Alkalinity, 

dissolved

(Gran titration)

(mg/L as CaCO3

)

Chloride,

dissolved

(mg/L as Cl)

4S/1W-17M7 03/19/2002 330 76.1 32.7 1.94 58.8 1260 82.84S/1W-17M8 03/22/2002 230 53 23.7 1.59 59.3 1162 74.14S/2W-12K10 11/05/2002 350 96.3 26.4 2.11 61.1 273 77.84S/2W-13P4 03/27/2002 370 86.3 38.5 2.11 68.8 1243 1214S/2W-13P6 03/26/2002 530 141 42.3 2.71 46.3 1232 2334S/2W-13P7 03/27/2002 510 138 40.3 2.63 46.1 1228 1513S/2W-20L20 10/29/2002 180 46.4 15.4 1.76 67.8 205 463S/2W-29L6 10/30/2002 140 40.9 9.82 1.94 123 212 98.54S/1W-17M6 03/19/2002 390 103 31.4 2.39 42.7 1220 1314S/2W-2H1 03/20/2002 160 45 10.5 1.99 87 1207 62.34S/2W-3L1 03/27/2002 160 43.4 11.2 1.95 63.5 1173 49.34S/2W-4E1 10/30/2002 150 42.2 11.7 2.47 132 218 1224S/2W-4F3 03/21/2002 160 44.1 12.4 2.03 75 1187 66.24S/2W-4R1 10/29/2002 240 66.6 17.6 2.34 92.8 199 1334S/2W-10E4 11/04/2002 290 82.3 19.3 2.84 57.6 174 1184S/2W-12C1 03/20/2002 210 59.4 15.4 2.35 85.5 1237 1034S/2W-12K8 11/05/2002 130 34.7 9.81 1.98 84.6 196 39.44S/2W-13P5 03/26/2002 570 156 42.2 2.58 48.8 1173 3154S/2W-14D3 04/16/2003 66 19.7 4.05 2.06 110 180 45.84S/2W-14D4 11/06/2002 140 39.8 10.8 2.57 144 211 1364S/2W-15L5 10/29/2002 220 63.5 13.6 2.9 236 166 346Dry Creek near Union City 04/17/2003 230 54.3 23.6 1.34 44 218 27.8USGS 373425121582101 PRECIP 

SAMPLER ACWD ROOFTOP INFLATION BLDG A NILES

11/08/2002

—

—

—

—

—

—

—

Table 5–1. Physical property, major-ion, selected trace-element, and isotopic data for groundwater, stream-water, and precipitation samples collected and analyzed by the U.S. Geological Survey, southern East Bay Plain and Niles Cone groundwater subbasins, Alameda County, California, 2002–03.—Continued[Data analyzed by U.S. Geological Survey (USGS). Location of sites shown in figure 1. Abbreviations: A, at; ACWD, Alameda County Water District; BLDG, building; CaCO3, calcium carbonate; E, approximate value; hhmm, 24-hour time format in hours and minutes; mg/L, milligram per liter; mm/dd/yyyy, month/day/year; N, nitrogen; PO4, phosphate; SiO2, silicon dioxide; °C, degrees Celsius; μg/L, microgram per liter; μS/cm, microsiemen per centimeter at 25 °C; <, actual value less than value shown; —, no data]
Appendix 5 55

State

well 

number

Date

(mm/dd/yyyy)

Fluoride,

dissolved

(mg/L as F)

Silica,

dissolved

(mg/L as SiO2)

Sulfate,

dissolved

(mg/L as SO4)

Nitrogen, 

ammonia, 

dissolved

(mg/L as N)

Nitrogen, 

ammonia 

+ organic, 

dissolved

(mg/L as N)

Nitrogen, 

nitrate + nitrite, 

dissolved

(mg/L as N)

Nitrogen, 

nitrite, 

dissolved

(mg/L as N)

4S/1W-17M7 03/19/2002 0.1 18.3 86.2 <0.04 <0.1 1.63 <0.0084S/1W-17M8 03/22/2002 0.2 15.6 81.8 <0.04 <0.1 0.2 <0.0084S/2W-12K10 11/05/2002 <0.17 24.7 62.4 <0.04 <0.1 8.13 0.0594S/2W-13P4 03/27/2002 0.2 16.6 88.8 <0.04 <0.1 2.38 <0.0084S/2W-13P6 03/26/2002 0.1 20.3 65 <0.04 <0.1 3.75 <0.0084S/2W-13P7 03/27/2002 0.1 20.7 85.2 <0.04 <0.1 9.5 <0.0083S/2W-20L20 10/29/2002 0.31 21.4 42.2 0.06 E0.08 <0.06 <0.0083S/2W-29L6 10/30/2002 <0.17 24.8 50 <0.04 <0.1 0.11 <0.0084S/1W-17M6 03/19/2002 0.1 20.6 59.9 <0.04 E0.07 3.54 0.0244S/2W-2H1 03/20/2002 0.2 21.9 39.6 <0.04 <0.1 0.66 E0.0044S/2W-3L1 03/27/2002 0.2 21.5 37.4 <0.04 <0.1 0.91 <0.0084S/2W-4E1 10/30/2002 0.2 25.3 47.5 0.1 0.1 <0.06 <0.0084S/2W-4F3 03/21/2002 0.2 23.3 38.6 <0.04 <0.1 0.31 <0.0084S/2W-4R1 10/29/2002 <0.17 22.3 47.1 <0.04 <0.1 2.09 E0.0064S/2W-10E4 11/04/2002 <0.17 22.5 63.9 0.06 E0.08 0.11 <0.0084S/2W-12C1 03/20/2002 0.1 22.2 40.3 <0.04 <0.1 1.37 <0.0084S/2W-12K8 11/05/2002 <0.17 18.7 44 <0.04 <0.1 0.35 E0.0044S/2W-13P5 03/26/2002 E0.1 19.6 47 <0.04 <0.1 2.53 E0.0054S/2W-14D3 04/16/2003 0.18 21 50.8 0.07 E0.08 0.1 <0.0084S/2W-14D4 11/06/2002 0.18 21.1 54.2 <0.04 <0.1 <0.06 <0.0084S/2W-15L5 10/29/2002 <0.17 20.3 75.3 0.08 0.1 <0.06 <0.008Dry Creek near Union City 04/17/2003 0.32 14.8 53.4 <0.04 0.21 0.11 <0.008USGS 373425121582101 PRECIP 

SAMPLER ACWD ROOFTOP INFLATION BLDG A NILES

11/08/2002 — — — — — — —

Table 5–1. Physical property, major-ion, selected trace-element, and isotopic data for groundwater, stream-water, and precipitation samples collected and analyzed by the U.S. Geological Survey, southern East Bay Plain and Niles Cone groundwater subbasins, Alameda County, California, 2002–03.—Continued[Data analyzed by U.S. Geological Survey (USGS). Location of sites shown in figure 1. Abbreviations: A, at; ACWD, Alameda County Water District; BLDG, building; CaCO3, calcium carbonate; E, approximate value; hhmm, 24-hour time format in hours and minutes; mg/L, milligram per liter; mm/dd/yyyy, month/day/year; N, nitrogen; PO4, phosphate; SiO2, silicon dioxide; °C, degrees Celsius; μg/L, microgram per liter; μS/cm, microsiemen per centimeter at 25 °C; <, actual value less than value shown; —, no data]
56 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins State well number Date (mm/dd/yyyy) Phosphorous, total, dissolved (mg/L as P) Phosphorous, ortho, dissolved (mg/L as PO4) Solids, residue at 180 °C, dissolved (mg/L) Solids, sum of constituents, dissolved (mg/L) Arsenic, dissolved (μg/L as As) Barium, dissolved (μg/L as Ba) Boron, dissolved (μg/L as B) Bromide, dissolved (mg/L as Br) 4S/1W-17M7 03/19/2002 <0.06 0.02 532 522 0.5 106 455 0.29 4S/1W-17M8 03/22/2002 <0.06 <0.02 422 409 0.3 83 470 0.25 4S/2W-12K10 11/05/2002 E0.03 0.04 566 553 0.5 165 232 0.36 4S/2W-13P4 03/27/2002 <0.06 E0.02 617 580 0.4 56 508 0.47 4S/2W-13P6 03/26/2002 E0.03 0.03 883 709 1.1 268 315 1.14 4S/2W-13P7 03/27/2002 E0.04 0.04 725 667 1 265 383 1.43 3S/2W-20L20 10/29/2002 0.04 0.04 379 366 1.2 63 320 0.18 3S/2W-29L6 10/30/2002 0.08 0.09 483 479 0.5 90 461 0.4 4S/1W-17M6 03/19/2002 0.1 0.12 561 541 1.3 173 314 0.63 4S/2W-2H1 03/20/2002 E0.05 0.04 403 398 0.7 115 546 0.24 4S/2W-3L1 03/27/2002 E0.05 0.05 352 338 0.4 99 367 0.19 4S/2W-4E1 10/30/2002 0.12 0.12 523 517 0.8 97 430 0.51 4S/2W-4F3 03/21/2002 E0.04 0.06 386 377 1 96 309 0.27 4S/2W-4R1 10/29/2002 E0.04 0.04 528 513 0.8 147 323 0.48 4S/2W-10E4 11/04/2002 E0.03 0.03 491 474 1.6 165 279 0.51 4S/2W-12C1 03/20/2002 E0.05 0.05 475 479 0.8 136 379 0.41 4S/2W-12K8 11/05/2002 0.04 0.05 358 354 1.9 98 314 0.18 4S/2W-13P5 03/26/2002 <0.06 0.03 1,080 750 0.8 367 299 1.23 4S/2W-14D3 04/16/2003 0.07 0.07 368 364 4.3 48 341 0.18 4S/2W-14D4 11/06/2002 0.06 0.06 550 537 2.1 119 401 0.56 4S/2W-15L5 10/29/2002 0.05 0.05 882 861 2.1 105 545 1.33 Dry Creek near Union City 04/17/2003 E0.03 0.02 373 352 0.7 55 218 0.03 USGS 373425121582101 PRECIP SAMPLER ACWD ROOFTOP INFLATION BLDG A NILES 11/08/2002

—

—

—

—

—

—

—

—

Table 5–1. Physical property, major-ion, selected trace-element, and isotopic data for groundwater, stream-water, and precipitation samples collected and analyzed by the U.S. Geological Survey, southern East Bay Plain and Niles Cone groundwater subbasins, Alameda County, California, 2002–03.—Continued[Data analyzed by U.S. Geological Survey (USGS). Location of sites shown in figure 1. Abbreviations: A, at; ACWD, Alameda County Water District; BLDG, building; CaCO3, calcium carbonate; E, approximate value; hhmm, 24-hour time format in hours and minutes; mg/L, milligram per liter; mm/dd/yyyy, month/day/year; N, nitrogen; PO4, phosphate; SiO2, silicon dioxide; °C, degrees Celsius; μg/L, microgram per liter; μS/cm, microsiemen per centimeter at 25 °C; <, actual value less than value shown; —, no data]
Appendix 5 57

State

well 

number

Date

(mm/dd/yyyy)

Iodide, 

dissolved

(mg/L as I)

Iron, 

dissolved

(μg/L as Fe)

Manganese, 

dissolved

(μg/L as Mn)

Strontium, 

dissolved

(μg/L as Sr)

Delta 

deuterium

(per mil)

Delta 

oxygen-18

(per mil)

Carbon-14

(percent 

modern)

Carbon-13/

Carbon-12 

ratio

(per mil)

Radiocarbonage

(years before 

present)

4S/1W-17M7 03/19/2002 0.004 <10 0.2 850 –46 –5.91 99.78 –15.31 184S/1W-17M8 03/22/2002 0.035 <10 0.7 585 –43.6 –5.38 100.1 –12.04 04S/2W-12K10 11/05/2002 0.004 <10 21.6 1,140 –42.5 –6.25 83.27 –16.21 1,5004S/2W-13P4 03/27/2002 0.019 <10 4.2 879 –44.4 –5.78 96.8 –16.2 2604S/2W-13P6 03/26/2002 0.002 <10 12 1,800 –49.6 –6.51 86.42 –14.85 1,2004S/2W-13P7 03/27/2002 0.004 <10 0.3 1,690 –44.7 –6.14 90.18 –15.09 8303S/2W-20L20 10/29/2002 0.154 331 189 567 –45.3 –6.89 38.53 –15.01 7,7003S/2W-29L6 10/30/2002 0.465 17 86.3 512 –48.5 –7.2 23.92 –15.04 12,0004S/1W-17M6 03/19/2002 0.004 <10 25.7 1,330 –49.2 –6.81 76.98 –14.47 2,1004S/2W-2H1 03/20/2002 0.193 143 164 562 –46.2 –7.23 35.78 –14.52 8,3004S/2W-3L1 03/27/2002 0.148 <10 194 527 –49.8 –7.07 52.78 –13.65 5,1004S/2W-4E1 10/30/2002 0.539 45 49.5 585 –49.1 –7.27 22.48 –15.29 12,0004S/2W-4F3 03/21/2002 0.236 <10 141 527 –50.4 –7.13 49.6 –13.52 5,6004S/2W-4R1 10/29/2002 0.096 15 204 853 –46.6 –7.02 61.76 –13.64 3,9004S/2W-10E4 11/04/2002 0.483 E6 139 1,100 –48.8 –7.2 52.86 –14.04 5,1004S/2W-12C1 03/20/2002 0.255 48 217 735 –48.4 –7.11 48.38 –13.26 5,8004S/2W-12K8 11/05/2002 0.178 <10 74.5 457 –48.8 –7.12 45.35 –13.67 6,4004S/2W-13P5 03/26/2002 0.002 <10 21.6 2,100 –50.5 –7.01 85.54 –15.11 1,3004S/2W-14D3 04/16/2003 0.175 <10 24 318 –49.2 –7.14 49.43 –13.85 5,7004S/2W-14D4 11/06/2002 0.577 <10 75.5 552 –49.6 –7.33 20.55 –15.1 13,0004S/2W-15L5 10/29/2002 0.632 E10 82.9 972 –50.2 –7.32 16.04 –15.08 15,000Dry Creek near Union City 04/17/2003 0.004 <10 3.6 407 — — — — —USGS 373425121582101 PRECIP 

SAMPLER ACWD ROOFTOP INFLATION BLDG A NILES

11/08/2002 — — — — –45.8 –7.65 — — —

1Alkalinity calculated using incremental titration, as milligrams per liter.

Table 5–1. Physical property, major-ion, selected trace-element, and isotopic data for groundwater, stream-water, and precipitation samples collected and analyzed by the U.S. Geological Survey, southern East Bay Plain and Niles Cone groundwater subbasins, Alameda County, California, 2002–03.—Continued[Data analyzed by U.S. Geological Survey (USGS). Location of sites shown in figure 1. Abbreviations: A, at; ACWD, Alameda County Water District; BLDG, building; CaCO3, calcium carbonate; E, approximate value; hhmm, 24-hour time format in hours and minutes; mg/L, milligram per liter; mm/dd/yyyy, month/day/year; N, nitrogen; PO4, phosphate; SiO2, silicon dioxide; °C, degrees Celsius; μg/L, microgram per liter; μS/cm, microsiemen per centimeter at 25 °C; <, actual value less than value shown; —, no data]
58 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins
Appendix 6 59

Appendix 6. Noble Gas and Tritium Data for Groundwater Samples Collected 

and Analyzed by the U.S. Geological Survey

Appendix 6

Table 6–1. Noble gas and tritium data for groundwater samples collected from selected wells in the Niles Cone and southern East Bay 

Plain groundwater subbasins, Alameda County, California, March–October, 2002–03.

[cm3/kg, cubic centimeter per kilogram; ID, identification; mm/dd/yyyy, month/day/year; nd, not determined; RA, 3He/4He ratio of air (1.84×10–6); Rs, 3He/4He 

ratio of sample; USGS, U.S. Geological Survey; μcm3/kg, micro-cubic centimeter per kilogram; +/–, plus or minus; <, less than; >, greater than; *, helium-4 age 

calculated with crustal flux (J0) = 3.0×10–6; Δ Ne, excess air (neon oversaturation); —, no data]

State 

well 

number

USGS 

site 

ID

Sample 

date

(mm/dd/yyyy)

Noble gas recharge 

temperature, in 

degrees Celsius

Salinity, in 

grams per 

kilograms

RS/RA

Helium-3 

(

3

He), in 

× 10–8 μcm3/kg

Helium-4 

(

4

He) 

in μcm3/kg

Neon 

(Ne), 

in μcm3/kg

Upper aquifer system

4S/1W-17M7 373457122002102 03/19/2002 15.4 +/– 0.8 0.51 1.30 17.8 98.7 374.4

4S/1W-17M8 373457122002103 03/22/2002 19.2 +/– 0.8 0.42 1.03 8.9 62.5 255.7

4S/2W-13P4 373447122021904 03/27/2002 11.4 +/– 0.7 0.61 1.68 20.8 89.2 340.4

4S/2W-13P6 373447122021902 03/26/2002 16.6 +/–0.9 0.76 2.22 37.9 123.1 430.1

4S/2W-13P7 373447122021903 03/27/2002 10.6 +/– 0.7 0.72 1.97 27.1 99.3 394.7

Deep aquifer

3S/2W-20L20 373912122065001 10/29/2002 15.5 +/– 0.7 0.38 0.91 8.3 66.0 248.0

3S/2W-29L6 373832122064801 10/30/2002 18.1 +/– 0.8 0.50 3.80 841.1 1599.9 286.6

4S/1W-17M6 373457122002101 03/19/2002 12.0 +/– 0.7 0.56 2.16 23.8 79.4 314.4

4S/2W-10E4 373601122042901 11/04/2002 14.3 +/– 0.8 0.48 4.16 1,494.6 2595.3 320.5

4S/2W-12C1 373620122015901 03/20/2002 10.1 +/– 0.7 0.48 4.05 480.7 857.8 320.4

4S/2W-12K8 373545122015001 11/05/2002 13.1 +/– 0.7 0.36 4.05 889.6 1586.6 246.9

4S/2W-13P5 373447122021901 03/26/2002 15.9 +/– 0.8 0.85 2.33 31.9 98.9 352.6

4S/2W-15L5 373457122041001 10/29/2002 10.5 +/– 0.9 0.93 4.21 2,396.4 4108.9 395.5

4S/2W-02H1 373648122023601 03/20/2002 14.1 +/– 0.7 0.41 3.83 436.9 824.6 327.2

4S/2W-03L1 373646122042701 03/27/2002 13.5 +/– 0.7 0.35 3.89 437.1 811.7 260.9

4S/2W-04E1 373708122055101 10/30/2002 16.7 +/– 0.8 0.53 4.00 1,130.1 2042.8 286.0

4S/2W-04F6 — 10/31/2002 15.1 +/– 0.8 0.33 3.39 254.9 544.1 297.2

4S/2W-04R1 373638122045901 10/29/2002 15.4 +/– 0.8 0.54 4.08 292.6 518.2 364.1

4S/2W-14D3 373521122033101 04/16/2003 13.4 +/– 0.7 0.36 4.25 2,274.9 386.0 240.0
60 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

State 

well 

number

USGS 

Site 

ID

Sample 

date

(mm/dd/yyyy)

Krypton 

(Kr), 

in μcm3/kg

Argon 

(Ar), 

in cm3/kg)

∆ Ne 

(percent)

Helium-4 (4He) 

Age*, in years 

before present

Tritium, 

in tritium 

units

Tritium/Helium-3 

residence times, in 

years before present

Upper aquifer system—Continued

4S/1W-17M7 373457122002102 03/19/2002 90.1 0.434 94.9 2 22.9 22

4S/1W-17M8 373457122002103 03/22/2002 80.8 0.374 37.3 <1 7.2 6

4S/2W-13P4 373447122021904 03/27/2002 99.0 0.428 71.0 9 32.5 27

4S/2W-13P6 373447122021902 03/26/2002 91.6 0.452 126.1 26 22.1 47

4S/2W-13P7 373447122021903 03/27/2002 102.0 0.478 96.7 <1 46.6 27

Deep aquifer—Continued

3S/2W-20L20 373912122065001 10/29/2002 80.9 0.375 29.2 12 0.6 nd 

3S/2W-29L6 373832122064801 10/30/2002 78.3 0.384 52.5 4425 <0.2 >50

4S/1W-17M6 373457122002101 03/19/2002 93.1 0.430 58.8 <1 16.6 43

4S/2W-10E4 373601122042901 11/04/2002 89.1 0.413 65.2 7287 <0.2 >50

4S/2W-12C1 373620122015901 03/20/2002 100.2 0.434 58.9 2255 7.8 >50

4S/2W-12K8 373545122015001 11/05/2002 85.4 0.396 25.9 4425 <0.2 >50

4S/2W-13P5 373447122021901 03/26/2002 87.9 0.420 84.2 21 10.0 58

4S/2W-15L5 373457122041001 10/29/2002 87.8 0.429 109.4 11612 <0.2 >50

4S/2W-02H1 373648122023601 03/20/2002 87.2 0.443 68.5 2145 <0.2 >50

4S/2W-03L1 373646122042701 03/27/2002 86.6 0.390 33.6 2166 <0.2 nd 

4S/2W-04E1 373708122055101 10/30/2002 80.8 0.392 50.4 5711 <0.2 >50

4S/2W-04F6 — 10/31/2002 85.8 0.398 54.3 1358 <0.2 >50

4S/2W-04R1 373638122045901 10/29/2002 89.6 0.427 89.5 1228 <0.2 >50

4S/2W-14D3 373521122033101 04/16/2003 84.4 0.386 22.2 11034 0.4 >50

Table 6–1. Noble gas and tritium data for groundwater samples collected from selected wells in the Niles Cone and southern East Bay 

Plain groundwater subbasins, Alameda County, California, March–October, 2002–03.—Continued

[cm3/kg, cubic centimeter per kilogram; ID, identification; mm/dd/yyyy, month/day/year; nd, not determined; RA, 3He/4He ratio of air (1.84×10–6); Rs, 3He/4He 

ratio of sample; USGS, U.S. Geological Survey; μcm3/kg, micro-cubic centimeter per kilogram; +/–, plus or minus; <, less than; >, greater than; *, helium-4 age 

calculated with crustal flux (J0) = 3.0×10–6; Δ Ne, excess air (neon oversaturation); —, no data]
Appendix 7 61

Appendix 7. Measured and Interpreted Carbon-13 and Carbon-14 Data for Groundwater Samples Collected and Analyzed by the U.S. Geological Survey

Appendix 7

Table 7–1. Measured and interpreted carbon-13 and carbon-14 data for groundwater samples collected from selected wells in the Niles Cone and southern East Bay Plain groundwater subbasins, Alameda County, California, March–October, 2002.[m, meter; pmC, percent modern carbon; *, data interpreted using the NETPATH computer program (Plummer and others, 1991); **, uncorrected ages calculated using the calculated Ao value of 69.37 pmC]

State 

well 

number

Local name

Distance 

along 

flow path, 

in feet

Well construction Carbon-13/carbon-12, in per mil Carbon-14

Top of screened 

interval, in feet 

below land 

surface

Bottom of 

screened 

interval, in feet 

below land 

surface

Measured Interpreted*

Measured, 

in percent 

modern carbon

Uncorrected 

age**, 

in years 

before present

Interpreted 

age*, 

in years 

before present

Interpreted 

groundwater 

flow rate, in 

feet per year

4S/2W-12K8 Pacific 0 470 510 –13.67 — 45.35 — 0 —4S/2W-12C1 Whipple 2,800 410 487 –13.26 –12.99 48.38 2,979 830 3.374S/2W-3L1 Danone 14,100 367 442 –13.65 –14.08 52.78 2,259 1,963 9.974S/2W-4F3 Well B 18,700 440 525 –13.52 –14.00 49.60 2,773 2,358 11.64S/2W-4E1 Well E 21,000 470 525 –15.29 –15.34 22.48 9,315 7,340 0.463S/2W-29L6 Mt. Eden 29,500 480 580 –15.04 –15.12 23.92 8,802 7,121 38.8

State well 

number

Mass transfer and cation exchange, 

in millimoles

Silicates Carbonates Cation exchange Clay precipitation Carbon Hydrogen sulfide (H2S) Gypsum

4S/2W-12K8 — — — — — — —4S/2W-12C1 0.17433 0.24003 0.01984 –0.14517 0.49844 –0.25078 0.21234S/2W-3L1 0.15806 –0.17239 –0.45914 –0.13475 0.11315 –0.07064 0.001894S/2W-4F3 0.09995 0.00217 –0.20884 –0.06165 0.16557 –0.08435 0.028124S/2W-4E1 2.37506 –0.34908 –0.1557 –3.50761 0.84418 –0.42209 0.458623S/2W-29L6 1.67357 –0.26514 –0.00092 –2.45955 0.71404 –0.35702 0.41957
62 Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain Groundwater Subbasins

Table 7–2. Chemical reactions used to interpret carbon-14 data.

Process Representative chemical equation Comments

Cation exchange (Ca, Mg)+2 + Na2•clay ↔ 2Na+ + (Ca, Mg)•clay Simulated as exchange of equal parts dissolved Ca+2

and Mg+2 for each part Na+ on the clay-exchange 

sites.

Carbonate precipitation HCO3

–

 + Ca+2 ↔ CaCO3 + H+

and

HCO3

–

 + Mg+2 ↔ MgCO3 + H+

Simulated as separate phases. Precipitation of only 

small amounts of MgCO3 were needed to balance 

the mass-balance model. In the environment, Mg+2

probably substitutes for Ca+2 in variable amounts 

within carbonate minerals.

Silicate weathering CaAl2Si2O8 + 8H+ → Ca+2 + 2Al+3 + 2H4SiO40

and

NaAlSi3O8 + 4H2O + 4H+ → Al3+ + 3H4SiO40 + Na+

and

KAlSi3O8 + 4H2O + 4H+ → Al+3 + 3H4SiO40 + K+

Simulated as dissolution of anorthite with smaller 

amounts of albite and potassium feldspar included 

to satisfy mass-balance constraints. In some settings, 

dissolution of chlorite or sepiolite also may occur. 

Although other primary silicates also may dissolve, 

thermodynamic data show that the system is 

supersaturated with respect to biotite (mica) and that 

dissolution of this mineral will not occur.

Sulfate reduction 2CH2O + SO4

–2 → HS–

 + 2HCO3

–

 + H+ Simulated as oxidation of organic matter having a δ13C 

of –21 per mil. 

Clay precipitation 0.33Na+ + 2.33Al(OH) + 3.67H4SiO40 + 2H+ → 

Na0.33Al2.33Si3.67O10(OH)2 + 12H2O

or

2Al+3 + H2O + 2H4SiO40 → Al2Si2O5(OH)4 + 6H+

Only small differences in mass transfer result from 

simulation of clay precipitation as montmorillonite 

or as kaolinite. Both minerals detected by X-ray 

diffraction.
Publishing support provided by the U.S. Geological Survey 

Science Publishing Network, Sacramento Publishing Service Center

For more information concerning the research in this report, contact the

 Director, California Water Science Center

U.S. Geological Survey

6000 J Street, Placer Hall

Sacramento, California 95819

https://ca.water.usgs.gov ISSN 2328-0328 (online)

https://doi.org/10.3133/sir20185003
Teague and others—Hydrogeologic Controls and Geochemical Indicators of Groundwater Movement in the Niles Cone and Southern East Bay Plain 

Groundwater Subbasins, Alameda County, California (ver. 1.1, February 2019)—Scientific Investigations Report 2018–5003

ISSN 2328-0328 (online)

https://doi.org/10.3133/sir20185003