U.S. GEOLOGICAL SURVEY

Water-Resources Investigations Report

Streamflow Gains and Losses along San Francisquito 

Creek and Characterization of Surface-Water and 

Ground-Water Quality, Southern San Mateo and 

Northern Santa Clara Counties, California, 1996–97

Prepared in cooperation with the

CITY OF MENLO PARK

02-4078

By Loren F. Metzger

Sacramento, California

2002

3015-19
U.S. DEPARTMENT OF THE INTERIOR

GALE A. NORTON, Secretary

U.S. GEOLOGICAL SURVEY

Charles G. Groat, Director

For additional information write to: Copies of this report can be purchased from:

U.S. Geological Survey

Information Services

Box 25286

Federal Center

Denver, CO 80225

The use of firm, trade, and brand names in this report is for identification purposes only and 

does not constitute endorsement by the U.S. Geological Survey.

District Chief

U.S. Geological Survey

Placer Hall, Suite 2012

6000 J Street

Sacramento, CA 95819-6129
Contents 3

CONTENTS

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

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

Previous Studies........................................................................................................................................................... 4

Acknowledgments ....................................................................................................................................................... 4

Physical Setting ..................................................................................................................................................................... 5

Surface-Water Hydrology............................................................................................................................................ 5

Ground-Water Hydrology............................................................................................................................................ 5

Measured Streamflow Gains and Losses ............................................................................................................................... 11

Methods of Data Collection and Analysis ................................................................................................................... 12

Streamflow Measurements and Estimated Gains and Losses...................................................................................... 14

Estimated Ground-Water Recharge from San Francisquito Creek.............................................................................. 22

Characterization of Surface-Water and Ground-Water Quality............................................................................................. 25

Methods of Water Sampling and Analysis................................................................................................................... 25

Major Ions.................................................................................................................................................................... 29

Surface Water..................................................................................................................................................... 29

Ground Water..................................................................................................................................................... 31

Oxygen-18 and Deuterium .......................................................................................................................................... 34

Summary and Conclusions .................................................................................................................................................... 38

References Cited.................................................................................................................................................................... 40

Appendix A. Field measurements and laboratory analyses of samples from ground-water wells, streamflowmeasurement stations, Lake Laguinta, and public supply, southern San Mateo and northern Santa Clara

Counties, California, 1996–97 ................................................................................................................................ 42

FIGURES

1. Map showing location of study area......................................................................................................................... 3

2. Map showing locations of streamflow-measurement stations and storm drains along San Francisquito 

Creek, southern San Mateo and northern Santa Clara Counties, California ............................................................ 6

3. Graph showing mean annual, annual mean, and monthly mean streamflow at U.S. Geological Survey 

(USGS) stream gage11164500 (site 3) on San Francisquito Creek at Stanford University, southern San Mateo

and northern Santa Clara Counties, water years 1932–41 and 1951–99 ................................................................. 7

4. Map showing locations of faults and geohydrologic sections along and perpendicular to San Francisquito

Creek, southern San Mateo and northern Santa Clara Counties, California ............................................................ 8

5. Generalized geohydrologic sections along and perpendicular to San Francisquito Creek, southern San Mateo

and northern Santa Clara Counties, California......................................................................................................... 9

6–9. Graphs showing:

6. Daily mean streamflow at U.S. Geological Survey (USGS) stream gage 11164500 (site 3) on San 

Francisquito Creek at Stanford University, southern San Mateo and northern Santa Clara Counties,

April 1, 1996, to May 31, 1997 ........................................................................................................................ 13

7. Streamflow measurements for the five seepage runs along San Francisquito Creek, southern San Mateo

and northern Santa Clara Counties, California ................................................................................................. 20

8. Average streamflow gains or losses by reach between sites 3 and 12 along San Francisquito Creek, 

southern San Mateo and northern Santa Clara Counties, California ............................................................... 21

9. Streamflow frequency for U.S. Geological Survey (USGS) stream gage 11164500 (site 3) on San 

Francisquito Creek, southern San Mateo and northern Santa Clara Counties, California, water years 

1932–41 and 1951–99 ...................................................................................................................................... 24
4 Contents

10. Map showing locations of ground-water, surface-water, and miscellaneous water-chemistry sampling sites,

southern San Mateo and northern Santa Clara Counties, California ....................................................................... 27

11. Trilinear diagram showing chemical composition of water from selected ground-water wells, streamflowmeasurement stations, Lake Lagunita, and public supply, southern San Mateo and northern Santa Clara

Counties, California, April 28 through May 2, 1997 ............................................................................................... 30

12. Graphs showing selected trace-element ratios as a function of chloride concentration in water from wells,

southern San Mateo and northern Santa Clara Counties, California, April 28 through May 2, 1997 ..................... 33

13. Graph showing relation between delta deuterium and delta oxygen-18 for (A) all water samples, (B) San 

Francisquito Creek and Arroyo Ojo de Agua Creek samples, and (C) ground-water samples from wells

along or near San Francisquito Creek, southern San Mateo and northern Santa Clara Counties, California,

April 1996 through May 1997 ................................................................................................................................. 35

14. Map showing delta oxygen-18 and delta deuterium for ground-water samples from wells along or near 

 San Francisquito Creek, southern San Mateo and northern Santa Clara Counties, California, April and 

 May 1997 ................................................................................................................................................................ 37

TABLES

1–5. Tables showing streamflow measurements and gain or loss of streamflow between stations, flow distance 

between stations, and rate of gain or loss of streamflow between stations along San Francisquito and Los 

Trancos Creeks, southern San Mateo and northern Santa Clara Counties, California:

1. April 29, 1996 ................................................................................................................................................. 15

2. June 13, 1996 .................................................................................................................................................. 16

3. July 22, 1996 .................................................................................................................................................. 17

4. February 25–27, 1997 .................................................................................................................................... 18

5. April 30, 1997 ................................................................................................................................................. 19

6. Estimated average streamflow gains and losses and estimated average annual streamflow loss, 

evapotranspiration loss, and ground-water recharge between sites 3 and 12 along San Francisquito Creek, 

southern San Mateo and northern Santa Clara Counties, California ...................................................................... 23

7. Summary of oxygen-18 and deuterium ratios in samples from ground-water wells, streamflowmeasurement stations, Lake Lagunita, and public supply, southern San Mateo and northern Santa Clara

Counties, California, 1996–97 ............................................................................................................................... 26

8. Construction data, depth to partly consolidated and consolidated bedrock assemblages, and aquifer zone of

ground-water wells used for water-chemistry sampling in southern San Mateo and northern Santa Clara

Counties, California................................................................................................................................................ 28
Contents 5

CONVERSION FACTORS, VERTICAL DATUM, WATER-CHEMISTRY UNITS, 

WATER YEAR DEFINITION, ABBREVIATIONS, AND WELL-NUMBERING SYSTEM

Temperature is given in degrees Celsius (oC) which can be converted to degrees Fahrenheit (oF) by the following equation: oF = 1.8(oC) + 32.

Vertical Datum

Sea level: In this report “sea level” refers to the National Geodetic Vertical Datum of 1929--a geodetic datum 

derived from a general adjustment of the first-order level nets of the United States and Canada, formerly called Sea 

Level Datum of 1929.

 Abbreviated Water-Chemistry Units

Chemical concentration is given in milligrams per liter (mg/L) or micrograms per liter (μg/L). Micrograms 

per liter is equivalent to “parts per billion.”An analysis expressed in milliequivalents per liter (meq/L) enables a 

easy determination of the relative proportions of ions in a water sample on the basis of equivalent weight instead 

of concentration. 

Specific conductance is given in microsiemens per centimeter at 25oC (μS/cm).

Stable-isotope data for oxygen and hydrogen are reported in delta ( ) notations as per mil (o/oo) parts per 

thousand.

Water Year

“Water year” refers to the 12-month period that starts October 1 and ends September 30; it is designated by 

the calendar year in which it ends.

Abbreviations

MEASERR, Computer program (MEASured ERRor)

USGS, U.S. Geological Survey

mmol, millimole

mmol/L, millimole per liter

Multiply By To obtain

Length

acre-foot (acre-ft) 0.001233 cubic hectometer 

acre-foot per day (acre-ft/d) 0.001233 cubic hectometer per day

acre-foot per day per mile [(acre-ft/d)/mi] 0.000766 cubic hectometer per second

acre-foot per year (acre-ft/yr) 0.001233 cubic hectometer per year

foot (ft) 0.3048 meter

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

foot per second (ft/s) 0.02832 meter per second 

cubic foot per second (ft3/s) 0.3048 cubic meter per second 

inch (in.) 25.4 millimeter

mile (mi) 1.609 kilometer

square mile (mi2) 259.0 hectare

δ
6 Contents

Well-Numbering System

Wells are identified and numbered according to their location in the rectangular system for the 

subdivision of public lands. Identification consists of the township number, north or south; the 

range number, east or west; and the section number. Each section is divided into sixteen 40-acre 

tracts lettered consecutively (except I and O), beginning with "A" in the northeast corner of the 

section and progressing in a sinusoidal manner to "R" in the southeast corner. Within the 40-acre 

tract, wells are sequentially numbered in the order they are inventoried. The final letter refers to 

the base line and meridian. In California, there are three base lines and meridians; Humbolt (H), 

Mount Diablo (M), and San Bernardino (S). All wells in the study area are referenced to the Mount 

Diablo base line and meridian (M). Well numbers consist of 15 characters and follow the format 

005S003W25G001M. In this report, well numbers are abbreviated and written 5S/3W-25G1. The 

following diagram shows how the number for well 5S/3W-25G1 is derived.

R5W R4W R3W

Meridian

 T4S

Mount Diablo

 T5S

 T6S

RANGE

TOWNSHIP

 R1W R1E

27

R3W

T5S

Well-numbering diagram

6 5 4 3 2 1

7

18 13

8 9 10 11 12

17 16 15 14

19 24

30 25

31 36

20 21 22 23

29 28 26

32 33 34 35

5S/3W-25G1

SECTION 25

D C B A

EFGH

M L K J

N P Q R
Abstract 1

Streamflow Gains and Losses along San Francisquito Creek 

and Characterization of Surface-Water and Ground-Water 

Quality, Southern San Mateo and Northern Santa Clara 

Counties, California, 1996–97

By Loren F. Metzger

ABSTRACT

San Francisquito Creek is an important 

source of recharge to the 22-square-mile 

San Francisquito Creek alluvial fan ground-water 

subbasin in the southern San Mateo and northern 

Santa Clara Counties of California. Ground water 

supplies as much as 20 percent of the water to 

some area communities. Local residents are 

concerned that infiltration and consequently 

ground-water recharge would be reduced if 

additional flood-control measures are 

implemented along San Francisquito Creek. To 

improve the understanding of the surfacewater/ground-water interaction between San 

Francisquito Creek and the San Francisquito Creek 

alluvial fan, the U.S. Geological Survey (USGS) 

estimated streamflow gains and losses along 

San Francisquito Creek and determined the 

chemical quality and isotopic composition of 

surface and ground water in the study area.

Streamflow was measured at 13 temporary 

streamflow-measurement stations to determine 

streamflow gains and losses along a 8.4-mile 

section of San Francisquito Creek. A series of five 

seepage runs between April 1996 and May 1997 

indicate that losses in San Francisquito Creek were 

negligible until it crossed the Pulgas Fault at Sand 

Hill Road. Streamflow losses increased between 

Sand Hill Road and Middlefield Road where the 

alluvial deposits are predominantly coarse-grained 

and the water table is below the bottom of the 

channel. The greatest streamflow losses were 

measured along a 1.8-mile section of the creek 

between the San Mateo Drive bike bridge and 

Middlefield Road; average losses between San 

Mateo Drive and Alma Street and from there to 

Middlefield Road were 3.1 and 2.5 acre-feet per 

day, respectively.

 Downstream from Middlefield Road, 

streamflow gains and losses owing to seepage may 

be masked by urban runoff, changes in bank 

storage, and tidal effects from San Francisco Bay. 

Streamflow gains measured between Middlefield 

Road and the 1200 block of Woodland Avenue 

may be attributable to urban runoff and (or) 

ground-water inflow. Water-level measurements 

from nearby wells indicate that the regional water 

table may coincide with the channel bottom along 

this reach of San Francisquito Creek, particularly 

during the winter and early spring when water 

levels usually reach their maximum. Streamflow 

losses resumed below the 1200 block of Woodland 

Avenue, extending downstream to Newell Road. 

Discharge from a large storm drain between 

Newell Road and East Bayshore Road may 

account for the streamflow gains measured 

between these sites. Streamflow gains were 

measured between East Bayshore Road and the 

Palo Alto Municipal Golf Course, but this reach is 

difficult to characterize because of the probable 

influence of high tides.

Estimated average streamflow losses totaled 

approximately 1,050 acre-feet per year for the 

reaches between USGS stream gage 11164500 at 

Stanford University (upstream of Junipero Serra 

Boulevard) and the Palo Alto Municipal Golf 
2 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Course, including approximately 595 acre-feet per 

year for the 1.8-mile section between San Mateo 

Drive and Middlefield Road. Approximately 

58 percent, or 550 acre-feet, of the total estimated 

average annual recharge from San Francisquito 

Creek occurs between the San Mateo Drive and 

Middlefield Road sites.

The chemical composition of San 

Francisquito Creek water varies as a function of 

seasonal changes in hydrologic conditions. 

Measurements of specific conductance indicate 

that during dry weather and low flow, the 

dissolved-solids concentrations tends to be high, 

and during wet weather, the concentration tends to 

be low owing to dilution by surface water. 

Compared with water samples from upstream sites 

at USGS stream gage 11164500 and San Mateo 

Drive, the samples from the downstream sites at 

Alma Street and Woodland Avenue had low 

specific conductance; low concentrations of 

magnesium, sodium, sulfate, chloride, boron, and 

total dissolved solids; high nutrient 

concentrations; and light isotopic compositions 

indicating that urban runoff constitutes most of the 

streamflow in some reaches during low flow.

The chemical composition of ground water 

in the study area varies primarily as a function of 

aquifer depth, changing from a calciumbicarbonate or mixed cation-bicarbonate water in 

the shallow aquifer to a sodium-chloride or mixed 

cation-mixed anion water in the lower zone of the 

deep aquifer. The most pronounced difference in 

ground-water composition between the shallow 

and deep aquifers occurs in the lower part of the 

San Francisquito Creek alluvial fan downstream of 

Alma Street owing to extensive deposits of bay 

mud and clay separating the two aquifers. The 

concentration of chloride in samples from some of 

the wells exceeds 100 milligrams per liter. Ratios 

of selected trace elements to chloride indicate that 

modern bay water intrusion is not the source of the 

high chloride concentrations: water moving 

through the deep aquifer may reach chloride-rich 

marine sediments where mineral dissolution may 

increase the concentrations of sodium and 

chloride.

Isotopic ratios of oxygen and hydrogen in 

water from selected surface-water sites, public 

supply, and selected production wells plot below, 

but parallel to, the global meteoric water line. The 

isotopically heaviest water was from Lake 

Lagunita and the isotopically lightest water was 

imported public supply water. With the exception 

of isotope samples collected from San Francisquito 

Creek at Alma Street and the 1200 block of 

Woodland Avenue during low-flow conditions, 

stream samples were isotopically heavier than 

ground-water samples. The isotopically heaviest 

ground-water samples were from wells near losing 

reaches of San Francisquito Creek. The 

isotopically lightest samples were from wells 

completed in the shallow aquifer and located close 

to residential streets. Water to these wells may be a 

mixture of native ground-water and imported water 

from leaking public water supply and sewage lines 

and return flow from excess irrigation of 

landscaping. The isotopic data also indicate that 

bay water intrusion is not the source of the high 

chloride concentrations in water from the wells 

sampled for this study.

INTRODUCTION

San Francisquito Creek, located in southern San 

Mateo and northern Santa Clara Counties (fig. 1), plays 

a vital role in the hydrology and ecology of these 

counties because it drains runoff from the Santa Cruz 

Mountains and downstream urban areas, provides 

wildlife habitat, and is an important source of 

ground-water recharge to the aquifers of the San 

Francisquito Creek alluvial fan. Streamflow in San 

Francisquito Creek originates as surface and shallow 

subsurface flow from winter and spring storms. As 

water flows downstream out of the Santa Cruz 

Mountains and across the San Francisquito Creek 

alluvial fan towards San Francisco Bay, some of it 

infiltrates through the streambed. Infiltration below the 

immediate subsurface soil zone that does not evaporate 

or that is not extracted by plant roots becomes 

ground-water recharge. Local residents are concerned 

that infiltration and consequently ground-water 

recharge would be reduced if additional flood-control 

measures are implemented along San Francisquito 

Creek.
Introduction 3

Figure 1. Location of study area.

122°17'30" 122°12'30" 122°07'30"

37°27'30"

37°20'

 San 

 Francisco

 Bay

 Palo Alto

 

Felt Lake

Lake

Lagunita

Searsville

Lake

 Crystal 

 Springs

 Reservoir

 Lower

 Emerald

 Lake

 Upper

 Emerald

 Lake

San Francisquito Creek alluvial fan—modified from California Department of Water Resources (1967)

San Francisquito Creek drainage basin—modified from U.S. Army Corps of Engineers (1972)

Contact between partly consolidated and consolidated bedrock assemblages (hachured side) and unconsoli-

 dated alluvium

Partly consolidated and consolidated bedrock assemblages

Study area boundary

Unconsolidated alluvium outside of San Francisquito Creek alluvial fan 

EXPLANATION

0

0

5 Miles

5 Kilometers

 Map

 area

Bear Gu lch

Creek

Los Trancos Creek

San Franci squito

Cree k

Atherton Channe l

West Union Creek

 Menlo

 Park

Woodside

Atherton

Bear Gulch

 Res.

 

Redwo od Creek

Barron Creek

Deer Creek

Matadero

Cre ek

 San 

Francisco

 Los 

Angeles

SANTA

CRUZ

MOUNTAINS

SAN MATEO CO

SANTA CLARA CO

Arroyo Ojo de Agua

—modified from Fio and Leighton (1995)

Hetch Hetchy

Reservoir

84

35

Redwood

 City

84

84 35

82

82

 C A L I F O R N I A

S I E R

R

A

N E

V E D

A

 STANFORD 

UNIVERSITY

SAN MATEO CO

SANTA CLARA CO

G5

G3

 East

 Palo Alto



11164500

 11164500 Stream-gaging station and identifier

Area of

figure 2

San Francisquito Cree k

280

280

101

101
4 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Since the 1960s, imported surface water has been 

the primary source of water supply in the study area. 

Ground water, however, is a significant source of water 

supply to some area communities; nearly 20 percent of 

the total water supply for the town of Atherton is 

ground water (Metzger and Fio, 1997). Excessive 

ground-water pumping or a reduction in ground-water 

recharge, or both, can cause water levels to decline and 

the quality of ground water to deteriorate. For example, 

from the 1900s through the mid 1960s, ground-water 

levels in parts of Palo Alto, Menlo Park, and Atherton 

declined below sea level, reversing hydraulic gradients 

and inducing the movement of saline water 2 to 3 mi 

inland from San Francisco Bay (Iwamura, 1980). 

Between 1934 and 1967, overdrafting of the aquifer 

system, combined with periodic drought, caused more 

than 2 ft of land subsidence in parts of Palo Alto and 

East Palo Alto (Poland and Ireland, 1988). In 1996, the 

U.S. Geological Survey (USGS), in cooperation with 

the city of Menlo Park, began a study to improve the 

understanding of the surface-water/ground-water 

interaction between San Francisquito Creek and the 

San Francisquito Creek alluvial fan. The objectives of 

the study were to provide quantitative information on 

streamflow gains and losses along San Francisquito 

Creek and to determine the chemical and isotopic 

composition of surface and ground water to help 

characterize surface- and ground-water quality in the 

study area. This report presents the results of that study.

Streamflow measurements made at 13 sites in 

1996 and 1997 were used to estimate gains and losses 

along selected reaches of San Francisquito Creek. 

Water samples collected from 17 wells, 9 streamflowmeasurement sites, and 3 miscellaneous surface-water 

sites were analyzed for chemical and isotopic 

composition. The chemical data were used to 

characterize the quality of surface and ground water 

and to help assess the source of ground water to wells.

Previous Studies

Several prior studies have focused on various 

aspects of the hydrogeology of the San Francisquito 

Creek area. During a comprehensive study of the San 

Francisquito Creek Basin, Sokol (1964) investigated 

the hydrogeology of the drainage basin and the alluvial 

fan. He used a volumetric approach to compile and sum 

sources of recharge to the alluvial fan and estimated 

recharge from all sources (seepage from San 

Francisquito Creek, seepage from Lake Lagunita, 

infiltration of runoff from the foothills not drained by 

San Francisquito Creek, overirrigation, infiltration of 

ground-water inflow from the foothills, and 

precipitation) at about 3,000 acre-feet/year (acre-ft/yr). 

According to Sokol, nearly 22 percent of this total, or 

about 650 acre-ft/yr, is seepage from San Francisquito 

Creek. This estimate is based on the difference in 

streamflow at USGS stream gage 11164500 [San 

Francisquito Creek at Stanford, Calif. (located at the 

Stanford University Golf Course)] and gage 11165500 

[San Francisquito Creek at Palo Alto, Calif. (located 

near Newell Road, not shown in figures)] from 1931 

and 1941, when both stations operated concurrently.

The spatial relation of well location, depth, and 

water quality was assessed during previous 

investigations. Results of an investigation in the Santa 

Clara Valley by Tolman and Poland (1940), which 

included the city of Palo Alto and Stanford University, 

indicate that saline water in shallow wells near San 

Francisco Bay is due to the encroachment of bay water 

through abandoned wells in the tidelands, through 

coarse-grained sediments near stream mouths, and 

through breaks in the clay aquiclude as a result of 

construction of the Dumbarton Bridge and the Hetch 

Hetchy pipeline. According to Sokol (1964), 

geophysical and drillers’ logs indicate that saline water 

measured in some deep wells located as much as 5 mi 

inland from the bay may originate from underlying 

marine deposits. Iwamura (1980) postulated that some 

parts of the deep aquifer have become saline as a result 

of the downward migration of bay water through wells 

screened in both shallow and deep aquifer zones. 

Metzger and Fio (1997), who investigated groundwater pumpage, ground-water levels, and ground-water 

quality in the town of Atherton, determined that the 

highest dissolved solids, sodium, and chloride 

concentrations were associated with samples from 

wells located closest to the foothills (approximately 

5 mi inland from the bay) and in the part of Atherton 

closest to the bay (less than 3 mi from the bay).

Acknowledgments

The author acknowledges the assistance of the 

Raychem Corporation, the city of Menlo Park, the city 

of East Palo Alto, the San Mateo County Department of 

Environmental Health Services, and the Santa Clara 

Valley Water District. Special thanks go to the city of 

Palo Alto Utilities Department, the O’Connor Tract 

Water Company, and the San Mateo County 

Department of Public Works, to private property owners 

for allowing access to wells, and to the Stanford 

University Facilities Operations staff for allowing 

access to wells and to Lake Lagunita.
Physical Setting 5

PHYSICAL SETTING

Southern San Mateo and northern Santa Clara 

Counties include the communities of Menlo Park, 

Atherton, Palo Alto, East Palo Alto, Redwood City, and 

Woodside, and Stanford University (fig. 1) and have a 

combined population of more than 200,000. Located 

25 to 30 mi south of San Francisco, the study area is a 

mixture of urban residential, commercial, industrial, 

and institutional development and open space. Most of 

the urban development is concentrated in the 

5-mile-wide alluvial plain situated between San 

Francisco Bay on the east and the foothills of the Santa 

Cruz Mountains on the west. Areas to the south and 

west of USGS stream gage 11164500, in the foothills of 

the Santa Cruz Mountains, are less developed than the 

areas on the alluvial plain and contain most of the study 

area’s remaining open space.

Surface-Water Hydrology

San Francisquito Creek flows northeast 12.7 mi 

(U.S. Army Corps of Engineers, 1972) from Searsville 

Lake to San Francisco Bay (fig. 1). Searsville Lake, a 

water-supply reservoir, is fed by intermittent streams 

that drain the eastern slope of the Santa Cruz 

Mountains. San Francisquito Creek and its tributaries, 

Bear Gulch and Los Trancos Creeks, drain a basin 

encompassing approximately 45 square miles (mi2

), 

including 37.4 mi2 of hilly to mountainous terrain 

upstream of USGS stream gage 11164500 and 

approximately 7.5 mi2

 of the San Francisquito alluvial 

fan, a gently sloping, mostly urbanized, plain extending 

downstream from USGS stream gage 11164500 to San 

Francisco Bay (fig. 1). Urban runoff from the 7.5 mi2 of 

the alluvial fan and from an additional area of several 

square miles outside the natural boundaries of the 

drainage area, including parts of Palo Alto, East Palo 

Alto, Stanford University, and Menlo Park, flows 

through storm drains to reach San Francisquito Creek.

Although San Francisquito Creek flows through 

an urban environment for most of its lower length, 

overall about half of the creek remains in a near-natural 

state. The lower 8.4 mi of San Francisquito Creek 

coincides with that part of the creek where 13 

temporary streamflow-measurement stations were 

established for this study (fig. 2). The streambed in this 

part of the creek consists of small boulders, cobbles, 

gravel, and sand upstream of El Camino Real (site 6) 

and grades to sandy silt and clay near the Palo Alto 

Municipal Golf Course (site 12) (fig. 2). In some 

reaches, the banks and channel of San Francisquito 

Creek are thickly vegetated with native alders, 

cottonwood, willows, oaks, and a variety of riparian 

plants, especially between Stanford University’s Webb 

Ranch (site 1) and several hundred feet downstream 

from site 4 near Sand Hill Road, and in parts of the 

creek between Middlefield Road (site 7) and Newell 

Road (site 10). As a result of damaging floods in 

February 1940, December 1955, and April 1958, 

concrete walls, earth berms, and concrete sack riprap 

lining were constructed along some reaches of San 

Francisquito Creek between El Camino Real and the 

mouth of the creek to reduce the threat of flooding to 

adjacent developed areas (U.S. Army Corps of 

Engineers, 1972).

Streamflow in San Francisquito Creek is variable 

owing to its dependence on rainfall. Average annual 

rainfall in the study area ranges from about 15 inches at 

Palo Alto for 1912–97 (California Department of Water 

Resources, 1981, microfiche records; National Oceanic 

and Atmospheric Administration, 1999) to more than 

40 inches at the highest elevations of the San 

Francisquito Creek drainage basin (Rantz, 1971). The 

variability of rainfall is reflected by the variability of 

monthly and annual streamflow records. The mean 

annual streamflow for the 59 years of available records, 

water years 1932–41 and 1951–99, for USGS stream 

gage 11164500 is 21.4 cubic feet per second (ft3

/s) 

(fig. 3). The annual mean streamflow for the period of 

this study, water years 1996 and 1997, was 35.8 and 

41.9 ft3

/s, respectively. Because approximately 

90 percent of annual rainfall in the study area occurs 

during November through April, most reaches of the 

creek on the San Francisquito Creek alluvial fan are dry 

about 6 months of the year. Upstream of the alluvial fan 

in the lower foothills of the Santa Cruz Mountains, 

ground-water seepage and treated wastewater from the 

Stanford Linear Accelerator (not shown in figures) 

located upstream of site 2 are sufficient to sustain flow 

at USGS stream gage 11164500 (site 3) throughout the 

drier months. Local residents have observed standing 

pools of water throughout the summer months during 

some years as far as several hundred yards downstream 

from site 4 (fig. 2).

Ground-Water Hydrology

Depositional and erosional processes during the 

Pleistocene and Holocene epochs gave rise to the 

present-day multiaquifer system in the study area 

(Sokol, 1964). The San Francisquito alluvial fan is an 

arbitrarily defined ground-water subbasin of the Santa 

Clara Valley, encompassing approximately 22 mi2

 in 

southern San Mateo and northern Santa Clara Counties 

(Sokol, 1964). The alluvial fan is bisected by San 
6 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Figure 2. Locations of streamflow-measurement stations and storm drains along San Francisquito Creek, southern San Mateo and northern 

Santa Clara Counties, California.

Woodside 

 

 Rd

El Camino Real

El Camino Real

Middlefield 

Middlefield 

 Lake 

Lagunita

Bear Gulch 

Reservoir

Embarcadero Embarcadero 

Alma 

 St



Page Mill Rd

 STANFORD 

GOLF COURSE

 WEBB RANCH

 (Stanford)

Sand Hill Rd

Pier St

El Camino

Real

Foothill

Exprwy

Arestradero

Rd

Bayshore

Bayshore

Freeway

Freeway

Rd

 PALO ALTO

GOLF COURSE

 MUNICIPAL

Charleston Rd

 Rd

San Antonio

Rd

Searsville

Lake

Junipero

Serra

Freeway

Sand 

Hill

Rd

Mt

Home Rd

Alpine Rd

Junipero Serra

Blvd

Santa Cruz Ave

Alpine Rd

San Francisquito

Creek

Los Trancos Cr

Marsh Rd

Atherton 

 

Ave

Alameda de las 

Woodside Rd

Whiskey Hill Rd

Stanford 

Ave

Jefferson

Ave

Bay

Bay

Rd

Rd

Whipple

Ave

El Camino

 Road

Far m

Hill Blv

Cr

Redwood

Cre ek

Arro yo Ojo de Ag ua

University

Ave

Matadero

Creek

Deer Cr

Barron 

Real

Atherton

Channel

Rd

Rd

Cordilleras

37°

30'

T 5 S

T 6 S

37°

27'

30"

37°

25'

0

0

1

1

2

2

3 Miles

3 Kilometers

Ravenswood Point

Creek

Pulgas

Adobe Creek

Newell

HETCH HETCHY

HETCH HETCHY

AQUEDUCT

AQUEDUCT





















 

 





1

2

4

11164500 3

11164500

LT

4

5

7 8 9

10

6

11

A11

A11

12

ADO

Sand Point

Rd

Dumbarton Bridge

Willow

Willow 

 Rd

Ringwood Ave

Middlefield 

 Road

University Ave

Ravenswood 

City Hall

City Hall

City Hall

Stanford University

SALT EVAPORATORS SALT EVAPORATORS

SALT EVAPORATORS

SALT EVAPORATORS

 SALT 

EVAPORATORS

Redwood City

Atherton

Menlo Park

Palo Alto

 East

 Palo Alto

San Francisco Bay

Bayfront Expwy

Ave

Hamilton

Chilco St

82

122°15' 122°12'30" 122°10'122° R 4 W R 3 W R 3 W 122°07'30" R 2 W

Base from U.S. Geological Survey

1:24,000 Palo Alto, 1991

Stream-gaging station and identifier (11164500) and temporary site identifier (3)—Site 3 is 

 a temporary streamflow measurement station adjacent to permanent stream-gaging station 

Temporary streamflow-measurement station and station identifier

EXPLANATION

Contact between partly consolidated and consolidated bedrock assemblages (hachured side)

 and unconsolidated alluvium —Modified from Fio and Leighton (1995)

3

84

San

Francisquito

Creek

SD

SD

Storm drain—Drain labeled A11 used as temporary streamflow-measurement station

Stanford diversion intake

San Mateo Dr

Woodland Ave

E. Bayshore Rd E. Bayshore Rd

280

101
Physical Setting 7

Francisquito Creek and several smaller creeks northwest and southeast of San Francisquito Creek (fig. 1). 

The alluvial fan, which trends southwest to northeast 

from the foothills of the Santa Cruz Mountains to 

within 1 mi of San Francisco Bay (fig. 1), was created 

by deposition of sediment from both the Santa Cruz 

Mountains and San Francisco Bay during interglacial 

periods of the Pleistocene and the postglacial 

Holocene (Sokol, 1964). These periods were marked 

by rising sea levels and consequent inundation of lowlands adjacent to San Francisco Bay. The inundations 

resulted in the deposition of sediments consisting predominantly of clay and silt. As sea levels declined during glacial periods, streams partly eroded the clay 

beds, depositing coarse-grained sediments in the channels and fine-grained sediments on the surrounding 

plain (Sokol, 1964).

Data from drillers’ logs of area wells were used 

to construct general geohydrologic sections to help 

define the aquifer system near San Francisquito Creek. 

Section A–A′, which runs along the bed of San 

Francisquito Creek, and sections B–B′ and C–C′, which 

run perpendicular to the creek (fig. 4), provide a 

generalized depiction of the geology of the study area 

(fig. 5). The aquifer system consists of a shallow aquifer 

that generally extends from near land surface to depths 

of about 15 to 100 ft below land surface, and a deep 

aquifer that has two water-bearing zones—an upper 

zone between about 200 and 300 ft below land surface 

and a lower zone that extends to depths greater than 

300 ft below land surface (fig. 5) (John Fio, U.S. 

Geological Survey, unpublished data, 1995).

Figure 3. Mean annual, annual mean, and monthly mean streamflow at U.S. Geological Survey (USGS) stream gage 11164500 (site 3) on San 

Francisquito Creek at Stanford University, southern San Mateo and northern Santa Clara Counties, California, water years 1932–41 and 

1951–99.

1930

1933

1936

1939

1942

1945

1948

1951

1954

1957

1960

1963

1966

1969

1972

1975

1978

1981

1984

1987

1990

1993

1996

1999

WATER YEAR

 Annual mean streamflow

Monthly mean streamflow

Mean annual streamflow for water years 1932–41 and 1951–99 (21.4 cubic feet per second)

MEAN STREAMFLOW, IN CUBIC FEET PER SECOND

0.01

1,000

0.02

0.03

0.04

0.05

0.07

0.1

0.2

0.3

0.4

0.5

0.7

1

2

3

4

5

7

10

20

30

40

50

70

100

200

300

400

500

700
8 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Figure 4. Locations of faults and geohydrologic sections along and perpendicular to San Francisquito Creek, southern San Mateo and 

northern Santa Clara Counties, California.

122°10' R 3 W 122°07'30" R 2 W

?

?

1

2

LT

3

4

4

5

7 8 9

10

6

12

Woodside 

 Rd

El Camino 

 Real

El Camino Real

Middlefield 

Middlefield 

 Lake 

Lagunita

Bear Gulch 

Reservoir

Embarcadero 

Embarcadero 

Alma 

 St

Page Mill Rd

 STANFORD 

GOLF COURSE

 WEBB RANCH

 (Stanford)

Sand Hill Rd

El Camino

Real

Foothill

Exprwy

Arestradero

Rd

Bayshore

Bayshore

Freeway

Freeway

Rd

 PALO ALTO

GOLF COURSE

 MUNICIPAL

Charleston Rd

San Antonio

Rd

Searsville

Lake

Junipero

Serra

Freeway

Sand 

Hill

Rd

Mt

Home

Rd

Alpine Rd

Junipero Serra

Blvd

Santa Cruz Ave

Alpine Rd

San Francisquito

Creek

Los Trancos Cr

Marsh Rd

Atherton 

 

 Ave

Woodside Rd

Whiskey Hill Rd

Stanford 

Ave

Jefferson

Ave

Bay

Bay

Rd

Rd

Whipple

Ave

El Camino

 Road

Far m

Hill Blv

Cr

Redwood

Cre ek

Arro yo O oj de Ag ua

University

Ave

Matadero

Creek

Deer Cr

Barron 

Rd

Real

Atherton

Channel

Rd

Rd

Cordilleras

37°

30'

T 5 S

T 6 S

37°

27'

30"

37°

25'

0

0

1

1

2

2

3 Miles

3 Kilometers

Ravenswood Point

Creek

Adobe Creek

Newell

3M2 3M10 36D1 Shallow aquifer Deep aquifer–upper zone Deep aquifer–lower zone

HETCH HETCHY

HETCH HETCHY

AQUEDUCT

AQUEDUCT

Sand Point

11 

Rd

					



Willow

Willow Rd

Ringwood Ave

Middlefield 

 Road

University Ave

Ravenswood 

City Hall

City Hall

City Hall

Stanford University

SALT EVAPORATORS SALT EVAPORATORS

SALT EVAPORATORS

SALT EVAPORATORS

Redwood City

Atherton

Menlo Park

Palo Alto

 East

 Palo Alto

San Francisco Bay

Bayfront Expwy

Ave

Hamilton

Chilco St

122°12'30"

84 



 

Base from U.S. Geological Survey

1:24,000 Palo Alto, 1991

 82



122°15' R 4 W R 3 W

 SALT 

 EVAPORATORS



?

?



3

Geophysically inferred; queried where uncertain

Geologically inferred; queried where uncertain

B B'

Temporary streamflow-measurement station and station identifier

Well and number—Abbreviated number does not include township and range designations 

Faults—Modified from Pampeyan (1993)

Line of geologic section B to B'—Perpendicular endcaps on San Francisquito Creek denote beginning and end of section. Line of section A to A' runs along the bed of the creek and extends into the bay

EXPLANATION

Contact between partly consolidated and consolidated bedrock assemblages (hachured side)

 and unconsolidated alluvium—Modified from Fio and Leighton (1995)

Atherton Fault

Atherton Fault

B

B'





C'

C

Pulgas Fault

San Francisquito 

 Fault

San Francisquito

Creek

27G1

27K2

27R3

35D3

34H1

35G10

36D1

36F2

36L10

1B2

2H10

1G1

11B10

3M2

3M10

25F1

25G1











Woodland

Ave E. Bayshore Rd E. Bayshore Rd

San Mateo Dr

Pier St

280

101

11164500

11164500

Stream-gaging station and identifier (11164500) and temporary site identifier (3)—Site 3 is 

 a temporary streamflow measurement station adjacent to permanent stream-gaging station 
Physical Setting

9

Figure 5. Generalized geohydrologic sections along and perpendicular to San Francisquito Creek, southern San Mateo and northern Santa Clara Counti

Rewis, U.S. Geological Survey)

D-L D-L

S S

-9' est -2' est 22' 14' est

 25'

? ? D-U

D-U

FEET

Site 4 at Pulgas Fault

Site 6 

Site 7

Site 8

Site 9

Site 10

Site 11

Site 12

Site 5 

Site 3 (USGS stream

 gage 11164500)

Atherton Fault

San Francisquito Fault

Hwy 101 

 Sea  level

 1,200

 300 200

 200

 100

 100

300

 900

 1,000

 1,100

 400

 500

 600 700

 800

5S/3W-34H1 (projected)

5S/3W-35G10

5S/3W-36D1 (projected)

5S/3W-36F2

6S/3W-3M10

6S/3W-3M2

SW 

bottom

Channel

B-B'

C-C'

A 

0

0

1

1

2 Kil

VERTICAL SCALE GREATLY EXAGGERATED

? ?
10 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97 Figure 5. Continued.18' 19' 17' 22' 10' B B' C C' Aquifers Shallow Deep-upper Deep-lower

S

D-U

D-U D-U

D-L

D-L D-L

S

S

Older, more co fine-grained al

Partly consolid

bedrock assem

Well and numb

5S/3W-36F2 (projected)

5S/3W-36L10

5S/3W-36L10

6S/3W-1B2 

6S/3W-1G1

Water-level alt sea level. Estim are based on m at some time d years. Queried 

0

0

1

1

2 Miles

2 Kilometers

FEET FEET

 Sea level

100

 900

 1,000

 1,100

 1,200

 100

 200

 300

 400

 500

 600

 700

 800

 Sea level

 1,200

100

 900

 1,000 1,100

 100

 200

 300

 400

 500

 600

 700

 800

5S/3W-27G1 (projected)

5S/3W-27K2 (projected)

5S/3W-27R3 (projected)

5S/3W-35D3 

5S/3W-34H1 (projected) NW SE NW SE

Undifferentiate coarse-grained 

EXPLA

Younger, predo grained alluviu

Coarse-grained 

VERTICAL SCALE GREATLY EXAGGERATED

Screened intescreened over 

Fine to medium

??

Geophysically 

Geologically 

Faults—Modif

-9'est. 14' -6'est.

14'

 Land surface Land surface

15'
Measured Streamflow Gains and Losses 11

The shallow aquifer consists of predominantly 

medium-grained alluvium (fine sand, silt, and clayey 

silt) deposited by San Francisquito Creek and smaller 

area creeks during the Holocene epoch. The upslope 

areas of the San Francisquito alluvial fan consist of 

coarser grained stream deposits. The thicknesses and 

grain sizes of these deposits are greatest near the 

mountain front and generally decrease towards San 

Francisco Bay. In areas within about 1 mi of San 

Francisco Bay, the alluvium is overlain by bay deposits, 

including silty clay, bay mud, and peat.

A thick, laterally extensive layer of bay deposits, 

consisting of undifferentiated clay interbedded with 

some lenses of coarse-grained alluvium, acts as a 

confining bed, separating the shallow aquifer from the 

deep aquifer throughout much of the northeastern part 

of the study area (fig. 5). Well logs indicate that this 

confining bed ends approximately midway between 

sites 5 and 6 on San Francisquito Creek, providing 

areas upslope of this confining bed with a direct 

hydraulic connection to the deep aquifer of the San 

Francisquito Creek alluvial fan (Sokol, 1964).

The deep aquifer consists of older alluvial 

deposits of gravel, sand, and silt of Pliocene and 

Pleistocene ages (John Fio, U.S. Geological Survey, 

unpublished data, 1995). The upper and lower zones of 

the deep aquifer are distinguished by differences in 

grain sizes; the upper zone generally has a greater 

proportion of coarse-grained alluvium than the lower 

zone.

Underlying the deep aquifer are partly 

consolidated to consolidated sedimentary and igneous 

rocks of the Franciscan Complex dating to the Jurassic 

and Cretaceous Periods, and sandstone consisting of 

interbedded siltstones and shales of the Tertiary Period 

(Pampeyan, 1993).

A series of faults in the study area may influence 

the hydrology of the multiaquifer system. The largest of 

these, the Pulgas Fault (at site 4 on figure 5), is a buried 

southwest-dipping reverse fault separating partly 

consolidated and consolidated bedrock assemblages on 

the southwest from younger unconsolidated alluvium 

on the northeast (fig. 4) (Pampeyan, 1993). Just 

northwest of San Francisquito Creek, the Pulgas Fault 

splits into two splays before merging southeast of the 

creek on the Stanford University campus (Pampeyan, 

1993). Results of a gravity study by Carle and others 

(1990) indicates the presence of two additional faults; 

the Atherton Fault and the San Francisquito Fault 

(fig. 4). The Atherton Fault extends from near Arroyo 

Ojo de Agua in Redwood City southeast towards 

Matadero Creek in Palo Alto. According to Carle and 

others (1990), the gravity gradient that defines the 

Atherton Fault becomes progressively weaker as it 

approaches the creek, indicating that the fault may be 

splintered or offset at San Francisquito Creek by a leftlateral “tear” fault called the San Francisquito Fault. 

Trending southwest to northeast along a northeasterly 

aligned depression in the partly consolidated and 

consolidated rock surface just south of San Francisquito 

Creek, the San Francisquito Fault may offset the 

Atherton Fault by about 1 mi so that on the northwest 

side the projection of the Atherton Fault intercepts the 

creek just above site 5 and, on the southeast side, it 

intercepts the creek approximately 0.3 mi upstream of 

El Camino Real (site 6, fig. 4). Unlike the Pulgas Fault, 

neither the Atherton Fault nor the San Francisquito 

Fault extends vertically through younger and older 

alluvium (Carle and others, 1990) (fig. 5). The Pulgas 

Fault may impede subsurface flow between the foothills 

and the alluvial fan.

There may be as many as 1,200 wells in the study 

area including residential wells (used primarily for 

landscape irrigation), municipal-supply wells, and 

observation wells (Metzger and Fio, 1997; David 

Leighton, U.S. Geological Survey, written commun., 

2000). Approximately 650 wells, including 500 wells in 

Atherton, are designated as production wells 

(irrigation, domestic, municipal, and institutional 

wells).

Prior to 1962, annual pumpage from the San 

Francisquito Creek alluvial fan was about 7,500 acre-ft, 

including about 6,500 acre-ft pumped by the city of 

Palo Alto and Stanford University (Sokol, 1964). Since 

the early- to mid-1960s, imported water from the Hetch 

Hetchy Aqueduct has largely replaced ground water as 

the primary source of municipal supply in the study 

area. Conversely, ground-water pumping by private 

residential wells has increased since the 1970s. Most of 

this increase has occurred in Atherton, where as many 

as 269 (“confirmed active” plus “probably active”) 

residential wells pumped an estimated 510 acre-ft/yr 

(Metzger and Fio, 1997). Nine institutional wells in 

Atherton may produce an additional 200 acre-ft/yr 

(Metzger and Fio, 1997). Based on limited well 

production information and extrapolation, 

ground-water pumping in the study area could total as 

much as 2,500 acre-ft/yr.

MEASURED STREAMFLOW GAINS AND LOSSES

Streamflow gains and losses along San 

Francisquito Creek were determined from streamflow 

measurements made during five seepage runs between 

April 1996 and May 1997. A seepage run consists of a 

series of streamflow measurements made at several 

sites along a stream to quantify streamflow gains and 
12 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

losses (Riggs, 1972). Intervals of a stream channel 

between successive measurement stations are referred 

to as either gaining or losing reaches. A gaining reach 

is defined as one in which streamflow increases in a 

downstream direction as a result of ground-water 

inflow, tributary inflow, or precipitation (Blodgett and 

others, 1992). In contrast, a losing reach is defined as 

one in which streamflow is lost by infiltration to the 

subsurface or by evapotranspiration to the atmosphere. 

If ground-water inflow is the only source of streamflow 

gain, it may be referred to as a seepage gain. A seepage 

loss refers to streamflow lost only by infiltration to the 

subsurface and not by direct evaporation.

Methods of Data Collection and Analysis

Streamflow was measured at 12 stations on San 

Francisquito Creek and at one station on Los Trancos 

Creek (LT) just above its confluence with San 

Francisquito Creek (fig. 2). Site 3 was established 

adjacent to a continuously recording stream gage 

(stream gage 11164500, San Francisquito Creek at 

Stanford) operated by the USGS. One temporary 

streamflow-measurement station, labeled A11 on 

figure 2, was established at the outfall of a storm drain 

to measure urban runoff entering the creek just 

upstream of site 11.

Streamflow was not measured or observed as not 

flowing at some of the 13 stations during three of the 

five seepage runs in 1996 and 1997 (June 13, 1996; 

July 22, 1996; and April 30, 1997). Streamflow was 

measured at all 13 stations during the other two seepage 

runs (April 29, 1996, and February 25–27, 1997). Flow 

conditions were arbitrarily defined for this study as 

low-flow, intermediate-flow, and high-flow conditions; 

the flow conditions were based on flow rates of 0 to 5, 

5 to 20, and greater than 20 ft3

/s, respectively, at USGS 

stream gage 11164500. The five seepage runs for this 

study included three low-flow seepage runs (June 13, 

1996; July 22, 1996; and April 30, 1997), one 

intermediate-flow seepage run (April 29, 1996), and 

one high-flow seepage run (winter flow uninfluenced 

by storms) (February 25–27, 1997).

Most streamflow measurements were made using 

velocity-area methods (for a description of these 

methods see Rantz and others, 1982). A Price pygmy 

current meter with a top-setting wading rod was used 

for the velocity-area methods. During low-flow 

conditions at stations where velocities were less than 

0.2 foot per second (ft/s) and stream depths were less 

than 0.3 ft, a modified 3-inch Parshall flume was used 

(Rantz and others, 1982).

Duplicate measurements were made by different 

hydrographers using different equipment at all the 

stations during the high-flow seepage run (February 

1997), at two stations during the intermediate-flow 

seepage run (April 1996), and at four stations during 

one low-flow seepage run (June 1996) to verify the 

repeatability of the measurements. High-flow stream 

measurements are particularly susceptible to error 

because the measurement error can exceed the 

calculated gain or loss if seepage gain or loss is small 

(Borchers, 1996). The average difference between 

duplicate measurements was about 5 percent; the 

largest difference between duplicate measurements was 

20 percent for site 5 for the April 1996 seepage run. 

Seepage runs were scheduled to avoid peak-flow 

conditions and periods of significant changes in stage, 

such as receding storm flows.

The accuracy of streamflow measurements is 

largely dependent on flow conditions and measurement 

technique (Rantz and others, 1982). For this study, the 

accuracy of streamflow measurements was assessed by 

examining streamflow conditions during each seepage 

run and by computing the uncertainty, or standard error, 

of each individual measurement.

Fluctuations in streamflow during a seepage run 

owing to either receding storm flows, diversions, or 

inflow from urban runoff can affect the accuracy of 

streamflow measurements and estimated seepage gains 

and losses. Records of instantaneous streamflow at 

USGS stream gage 11164500 were used to ascertain 

whether seepage runs had been completed during fairly 

stable flow conditions, at least in the upper reaches 

(sites 1 through 3) of San Francisquito Creek. 

Instantaneous records of USGS stream gage 11164500 

show minimal change in streamflow at that location 

during four of the five seepage runs (fig. 6), which 

indicates that streamflow was fairly stable at least in the 

reaches upstream of site 3. Streamflow at site 3 ranged 

from no change during the February and April 1997 

seepage runs to an approximately 20-percent decrease 

during the June 1996 seepage run. Because the June 

1996 seepage run coincided with a period of diversions 

from San Francisquito Creek to Lake Lagunita, the 

significant decrease in streamflow during that seepage 

run may have been caused by a sudden increase in the 

diversion rate.

The stability of streamflow in the middle (sites 3 

through 7) and lower reaches (sites 7 through 12) of San 

Francisquito Creek, below USGS stream gage 

11164500, was more difficult to ascertain because of 

the existence of large-diameter storm drains, which can 

carry flow to San Francisquito Creek independent of 

storm conditions. The locations of all storm drains 

terminating at San Francisquito Creek were not known 

prior to the seepage runs; where observed, urban runoff 

appeared to be restricted to the storm drains with 
Measured Streamflow Gains and Losses 13

diameters greater than approximately 30 inches. There 

are 12 storm drains between sites 3 and 12 (fig. 2) 

equal to or greater than 30 inches in diameter that may 

have affected the streamflow measurements. Discharge 

from the largest of these storm drains, which is at site 

A11 just downstream of East Bayshore Road, was 

measured only during the high-flow seepage run (February 25–27, 1997) because the contribution of this 

drain to the total streamflow was high.

The accuracy of the measurements obtained 

using the pygmy current meters and the modified 

3-inch Parshall flume was assessed by rating each 

individual streamflow measurement. The MEASERR 

(MEASurement ERRor) computer program (Sauer and 

Meyer, 1992) was used to determine the uncertainty or 

“error” of individual streamflow measurements 

obtained using pygmy current meters. This program 

assigns a corresponding qualitative rating (excellent, 

good, fair, or poor) for each streamflow measurement. 

Potential sources of error that may affect the rating 

include the type and operating condition of the current 

meter used, the number of measurement verticals in a 

cross section, the measurement time of each vertical, 

the mean velocity, the mean depth, the stability of the 

Figure 6. Daily mean streamflow at U.S. Geological Survey (USGS) stream gage 11164500 (site 3) on San Francisquito Creek at Stanford 

University, southern San Mateo and northern Santa Clara Counties, California, April 1, 1996, to May 31, 1997. Graph inserts show streamflow 

in cubic feet per second (ft3

/s).

APR MAY JUNE JULY AUG SEPT OCT NOV DEC JAN FEB MAR APR MAY 

1996 1997

0.1

10,000

0.2

0.3

0.4

0.5

0.7

1

2

3

5

7

10

20

30

40

50

70

100

200

300

400

500

700

1,000

2,000

3,000

4,000

5,000

7,000

DAILY MEAN STREAMFLOW, IN CUBIC FEET PER SECOND

INSTANTANEOUS

STREAMFLOW (ft3/s)

INSTANTANEOUS

STREAMFLOW (ft3/s)

INSTANTANEOUS

STREAMFLOW (ft3/s)

INSTANTANEOUS

STREAMFLOW (ft3/s)

INSTANTANEOUS

STREAMFLOW (ft3/s)

EXPLANATION

20

19 Feb 25 Feb 26 Feb 27

21

22

Instantaneous streamflow

Period of seepage-run measurements

5

6

7

8

April 28 April 29 April 30

1996 1996

1996

1997

1997

0

1

2

3

June 12 June 13 June 14

0

1

2

3

July 21 July 22 July 23

2

3

4

5

April 29 April 30 May 1
14 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

stream bottom, and the experience of the operator 

(Sauer and Meyer, 1992). Streamflow-measurement 

error ranged from good (2 to less than 5 percent) to 

poor (greater than 8 percent) for individual pygmy 

current meter measurements. Overall, 91 percent of the 

streamflow measurements made using the pygmy 

current meter had at least a fair measurement rating 

(measured discharge within 8 percent of ‘true’ 

discharge). In contrast, measurements made using the 

modified 3-inch Parshall flume generally were accurate 

to within 2 to 3 percent because of the fewer potential 

sources of error. The sources of error using the flume 

are limited mainly to flume installation, including 

leveling of the flume and minimizing leakage of water 

under and around it (Rantz and others, 1982).

The accuracy of the streamflow measurements 

was further assessed by comparing the pygmy 

current-meter measurements at the streamflowmeasurement station at site 3 with the instantaneous 

stream-gage records for USGS stream gage 11164500. 

The differences between the pygmy current meter 

measurements and the instantaneous stream-gage 

records were 1 percent for the April 1996 seepage run, 

less than 1 percent for the June 1996 seepage run, 

6 percent for the July 1996 seepage run, 11 percent for 

the February 1997 seepage run, and 37 percent for the 

April 1997 seepage run. The large difference for the 

April 1997 seepage run may be due to hydrographer 

error. Some differences, however, may be attributable 

to the broad-crested weir at USGS stream gage 

11164500; this type of control structure can be 

insensitive to low-flow conditions, especially during 

periods of warm weather when algae growth can occur 

on the weir’s upstream side. The growth of the algae 

can cause water to pool slightly behind the weir 

resulting in a slightly higher gage height. A few 

hundredths of a foot change in gage height can result in 

a large change in discharge (Rantz and others, 1982).

Streamflow gains and losses were calculated for 

each reach using streamflow measurements from 

successive stations. Duplicate measurements made 

during the same seepage run for individual sites were 

averaged prior to calculating gains and losses. The 

measurement error for the averaged measurements was 

determined by calculating the root mean square of the 

individual streamflow measurement errors. Measurable 

inflows to San Francisquito Creek from Los Trancos 

Creek and from the creek’s largest storm drain (A11) 

were subtracted from the downstream streamflow 

measurements, and reported diversions to Lake 

Lagunita on the Stanford University campus were 

added to the streamflow measurements to attain the 

most accurate calculations of streamflow gains and 

losses between stations.

Streamflow Measurements and Estimated Gains 

and Losses

Streamflow measurements, gains or losses 

between stations, flow distances, and rates of gain or 

loss of flow are shown in tables 1–5 for the five seepage 

runs. Streamflow as a function of stream distance 

downstream from Searsville Lake is depicted 

graphically in figure 7.

As shown in figure 7, San Francisquito Creek 

generally is a losing stream downstream from site 4 for 

all flow regimes. Streamflow gains between some 

stations during several seepage runs were attributed to 

urban runoff, water released from bank storage, and 

ground-water underflow after inflows from Los Trancos 

Creek (LT) and the storm drain at site A11 had been 

subtracted.

Average streamflow losses upstream of site 3 

were relatively small compared with losses downstream 

from site 3 when inflows from Los Trancos Creek and 

diversions by Stanford University are accounted for. 

Streamflow losses probably were small because the 

stream channel directly overlies low-permeability, 

partly consolidated and consolidated bedrock 

assemblages (figs. 5 and 7). Streamflow losses between 

sites 1 and 2 averaged 0.8 acre-foot per day (acre-ft/d) 

for the three seepage runs for which measurements 

were made at both sites (tables 1, 2, and 4). 

Downstream from site 2 at Pier Street, streamflow 

increased sharply for all seepage runs because of inflow 

from Los Trancos Creek, and decreased just upstream 

of site 3 at the Stanford University Golf Course during 

the April and June 1996 seepage runs because of 

diversions by Stanford University through creekside 

intake pumps (SD, Stanford diversion) a short distance 

upstream of site 3 (fig. 7). During the spring, several 

acre-feet per day are diverted to fill and maintain Lake 

Lagunita at or near its 360 acre-ft capacity (Sokol, 

1964; Marty LaPorte, Stanford University, written 

commun., 1997). Following commencement 

ceremonies at the university in mid-June, Lake 

Lagunita usually is drained to San Francisquito Creek 

through storm drains located upstream of site 6 (Larry 

Andrews, Stanford University Facilities Operations, 

oral commun., 1997). After accounting for inflow from 

Los Trancos Creek (+LT) and diversions from 

San Francisquito Creek to Lake Lagunita (−SD), losses 

between sites 2 and 3 were negligible, averaging only 

0.1 acre-ft/d for four of the seepage runs.

Downstream from site 3, the streambed overlies 

unconsolidated alluvium (figs. 5 and 7). Streamflow 

measurements made between sites 3 and 4 show slight 

gains during the June 1996 and February 1997 seepage 

runs and slight losses during the April and July 1996 
Measured Streamflow Gains and Losses 15

Table 1. Streamflow measurements and gain or loss of streamflow between stations, flow distance between stations, and rate of gain or loss of stream

Francisquito and Los Trancos Creeks, southern San Mateo and northern Santa Clara Counties, California, April 29, 1996

[See figure 2 for site locations. River distance, distance downstream from Searsville Lake. Measurement rating: excellent (less than 2 percent error), good (2 to less than 5 

poor (greater than 8 percent error). mi, mile; ft3/s, cubic foot per second; acre-ft/d, acre-foot per day; (acre-ft/d)/mi, acre-foot per day per mile. LT, Los Trancos; SD, Stan

Survey. na, not applicable]

1 Below the confluence of Los Trancos Creek and San Francisquito Creek. No measurement station at this location. Streamflow for this location was estimated from 

streamflow measurements (see footnote 2).

2 Summation of site 2 and site LT streamflow measurements.3 Above the Stanford diversion for Lake Lagunita. No measurement station at this location. Streamflow for this location was estimated from the summation of SD a

footnote 4).

4 Sum of streamflow for site 3 and the reported value for the SD site. Reported value from Marty LaPorte (Stanford University, written commun., 1997). 5 Reported value for Lake Lagunita diversion (Marty LaPorte, Stanford University, written commun., 1997).6 Average of two streamflow measurements by different hydrographers.7Rating based on root mean square of errors for two streamflow measurements.

Station River

distance 

(mi)

Streamflow Measurement

rating

Gain (+) or loss (−) 

of streamflow

between stations 

(acre-ft/d)

Flow d

bet

sta

(

Site 

identifier Location (ft3/s) (acre-ft/d)

1 Webb Ranch............. 2.7 6.46 12.8 Good na n2 Pier Street................. 3.7 6.22 12.3 Good −0.5 

LT Los Trancos Creek above confluence 

with San Francisquito Creek na 1.83 3.6 Fair na n

Below confluence1 ... 3.7 2 8.05 15.9 na +3.6 nAbove SD 3 ............. 4.7 4 7.43 14.7 na −1.2 

SD Stanford diversion for Lake Lagunita 4.7 5 .81 1.6 na na n

3 USGS stream gage 11164500

(Stanford Golf Course) 4.8 6.62 13.1 Good na 

4 Sand Hill Road......... 5.4 6 6.20 12.3 Fair7 −.8 5 San Mateo Drive bike bridge 6.3 6 5.96 11.8 Fair7 −.5 6 Alma Street .............. 7.4 3.83 7.6 Good −4.2 7 Middlefield Road ..... 8.1 2.49 4.9 Good −2.7 8 1200 block of Woodland Avenue 9.1 2.52 5.0 Fair +.1 9 University Avenue.... 9.7 1.90 3.8 Fair −1.2 

10 Newell Road ............ 10.0 2.14 4.2 Good +.5 11 East Bayshore Road. 10.7 2.64 5.2 Good +1.0 12 Palo Alto Municipal Golf Course 11.1 2.20 4.4 Good −.8 
16 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97 Table 2. Streamflow measurements and gain or loss of streamflow between stations, flow distance between stations, and rate of gain or loss of stream

Francisquito and Los Trancos Creeks, southern San Mateo and northern Santa Clara Counties, California, June 13, 1996 [See figure 2 for site locations. No streamflow at sites 10, 11, and 12. River distance, distance downstream from Searsville Lake. Measurement rating: excellent (less than 

percent error), fair (5 to 8 percent error), poor (greater than 8 percent error). mi, mile; ft3/s, cubic foot per second; acre-ft/d, acre-foot per day; (acre-ft/d)/mi, acre-foot per 

Stanford diversion; USGS, U.S. Geological Survey. na, not applicable]

1 Average of two streamflow measurements by different hydrographers.2 Rating based on root mean square of errors for two streamflow measurements.3 Below the confluence of Los Trancos Creek and San Francisquito Creek. No measurement station at this location. Streamflow for this location was estimated from 

measurements (see footnote 4).

4 Summation of site 2 and site LT streamflow measurements.5 Above the Stanford diversion for Lake Lagunita. No measurement station at this location. Streamflow for this location was estimated from the summation of SD a

measurements (see footnote 6).

6 Sum of streamflow for site 3 and the reported value for the SD site. Reported value from Marty LaPorte (Stanford University, written commun., 1997).7 Reported value for Lake Lagunita diversion (Marty LaPorte, Stanford University, written commun., 1997).8 Flume measurement.9 Based on measurement error for flume technique (Rantz and others, 1982). 

Station River

distance 

(mi)

Streamflow Measurement 

rating

Gain (+) or loss (−)

of streamflow 

between stations

(acre-ft/d)

Flow dist

between s

(mi)

Site 

identifier Location (ft3/s) (acre-ft/d)

1 Webb Ranch ............. 2.7 1 1.66 3.3 Fair 2 na na 2 Pier Street................. 3.7 1 1.86 3.7 Poor 2 +0.4 1.

LT Los Trancos Creek above confluence

with San Francisco Creek na 1.04 2.1 Poor na na 

Below confluence 3... 3.7 4 2.90 5.7 na +2.0 na Above SD 5............... 4.7 6 2.25 4.5 na −1.2 1.

SD Stanford diversion for Lake

Lagunita .................. . 4.7 7 1.07 2.1 na na na 

3 USGS stream gage 11164500 (Stanford

Golf Course)........ 4.8 1 1.18 2.3 Fair 2 na 1.

4 Sand Hill Road......... 5.4 1 1.33 2.6 Fair 2 +.3 .5 San Mateo Drive bike bridge 6.3 8 .26 .5 Good 9 −2.1 .6 Alma Street .............. 7.4 .00 .0 na −.5 1.7 Middlefield Road ..... 8.1 .00 .0 na .0 .8 1200 block of Woodland Avenue 9.1 8 .28 .6 Good 9 +.6 1.9 University Avenue.... 9.7 .00 .0 na −.6 .
Measured Streamflow Gains and Losses 17

Table 3. Streamflow measurements and gain or loss of streamflow between stations, flow distance between stations, and rate of gain or loss of stream

Francisquito and Los Trancos Creeks, southern San Mateo and northern Santa Clara Counties, California, July 22, 1996

[See figure 2 for site locations. Streamflow was nonexistent downstream from site 5 for unknown distance downstream. River distance, distance downstream from Searsv

(less than 2 percent error), good (2 to less than 5 percent error), fair (5 to 8 percent error), poor (greater than 8 percent error). mi, mile; ft3/s, cubic foot per second; acre-ft

foot per day per mile. LT, Los Trancos; USGS, U.S. Geological Survey. na, not applicable; —, no data available]

1 Not measured.2 Below the confluence of Los Trancos Creek and San Francisquito Creek. No measurement station at this location. Streamflow for this location was estimated from 

streamflow measurements (see footnote 3).

3 Summation of site 1 and site LT measurements.4 Streamflow gain between confluence of Los Trancos Creek and San Francisquito Creek and site 3.5 Flume measurement.6 Rating based on measurement error for flume technique (Rantz and others, 1982).

Station River

distance

(mi)

Streamflow Measurement

rating

Gain (+) or loss (−)

of streamflow

between stations

(acre-ft/d)

Flow distan

between

stations

(mi)

Site 

identifier Location (ft3/s) (acre-ft/d)

1 Webb Ranch ............. 2.7 0.27 0.5 Poor na na 2 Pier Street ................. 3.7 (1) — na — 1.0 

LT Los Trancos Creek above confluence 

with San Francisquito Creek na .44 .9 Poor na na 

Below confluence2 .... 3.7 3 .71 1.4 na na na 

3 USGS stream gage 11164500 

Stanford Golf Course) 4.8 1.04 2.1 Fair 4 +0.7 1.1 

4 Sand Hill Road ......... 5.4 .85 1.7 Fair −.4 .6 5 San Mateo Drive bike bridge 6.3 5 .09 .2 Good 6 −1.5 .9 6 Alma Street............... 7.4 .00 .0 na −.2 1.1 
18 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97 Table 4. Streamflow measurements and gain or loss of streamflow between stations, flow distance between stations, and rate of gain or loss of stream

Francisquito and Los Trancos Creeks, southern San Mateo and northern Santa Clara Counties, California, February 25

–27, 1997

[River distance, distance downstream from Searsville Lake. Measurement rating: excellent (less than 2 percent error), good (2 to less than 5 percent error), fair (5 to 8 per

error). mi, mile; ft3/s, cubic foot per second; acre-ft/d, acre-foot per day; (acre-ft/d)/mi, acre-foot per day per mile. LT, Los Trancos; USGS, U.S. Geological Survey. na, n

1 Average of two streamflow measurements by different hydrographers.2 Rating based on root mean square of errors for two streamflow measurements.3 Below the confluence of Los Trancos Creek and San Francisquito Creek. No measurement station at this location. Streamflow for this location was estimated from 

streamflow measurements (see footnote 4).

4 Summation of site 2 and site LT streamflow measurements.5 Measured discharge from outlet of 96-inch diameter storm drain at East Bayshore Road.6 Difference between measured storm drain discharge and site 11 streamflow measurement.

Station River

distance

(mi)

Streamflow Measurement 

rating

Gain (+) or loss (−)

of streamflow 

between stations 

(acre-ft/d)

Flow di

betw

stati

(m

Site 

identifier Location (ft3/s) (acre-ft/d)

1 Webb Ranch ............. 2.7 1 14.7 29.1 Fair 2 na na 2 Pier Street................. 3.7 1 13.5 26.7 Fair 2 −2.4 1.0 

LT Los Trancos Creek above confluence with San Francisquito Creek na 1 4.91 9.7 Fair 2 na na 

Below confluence3 .... 3.7 4 18.4 36.4 na +9.7 na 

3 USGS stream gage 11164500 (Stanford Golf Course) 4.8 1 19.0 37.6 Fair 2 +1.2 1.4 Sand Hill Road ......... 5.4 1 19.3 38.2 Fair 2 +.6 .6 5 San Mateo Drive bike bridge 6.3 1 19.1 37.8 Fair 2 −.4 .9 6 Alma Street .............. 7.4 1 17.8 35.2 Fair 2 −2.6 1.7 Middlefield Road...... 8.1 1 16.6 32.9 Fair 2 −2.3 .7 8 1200 block of Woodland Avenue 9.1 1 17.6 34.8 Fair 2 +1.9 1.0 9 University Avenue .... 9.7 1 16.6 32.9 Fair 2 −1.9 .6 

10 Newell Road............. 10.0 1 15.4 30.5 Fair 2 −2.4 .3 

A11 (Storm drain) 10.6 5 .45 0.9 na na na 

Above A11 10.6 6 15.4 30.5 na .0 .6 

11 East Bayshore Road . 10.7 1 15.8 31.3 Fair 2 +.8 .7 12 Palo Alto Golf Course 11.1 1 16.6 32.9 Fair 2 +1.6 .4 
Measured Streamflow Gains and Losses 19

Table 5. Streamflow measurements and gain or loss of streamflow between stations, flow distance between stations, and rate of gain or loss of stream

Francisquito and Los Trancos Creeks, southern San Mateo and northern Santa Clara Counties, California, April 30, 1997

[See figure 2 for site locations. Streamflow was nonexistent midway between sites 8 and 9 and at sites 10, 11, and 12. River distance, distance downstream from Searsvillexcellent (less than 2 percent error), good (2 to less than 5 percent error), fair (5 to 8 percent error), poor (greater than 8 percent error). mi, mile; ft3/s, cubic foot per secoft/d)/mi, acre-foot per day per mile. LT, Los Trancos; USGS, U.S. Geological Survey. na, not applicable; —, no data available]

1 Not measured.2 Below the confluence of Los Trancos Creek and San Francisquito Creek. No measurement station at this location.3 Loss of streamflow between stations 3 and 5.4 Seepage loss of 1.2 acre-ft/d between sites 3 and 5 divided between reaches 3 to 4 and 4 to 5 based on approximate proportions of other seepage losses for these p5 Flume measurement.6 Rating based on measurement error for flume technique (Rantz and others, 1982).

Station River

distance

(mi)

Streamflow Measurement

rating

Gain (+) or loss (−)

of streamflow

between stations

(acre-ft/d)

Flow dista

betwee

station

(mi)

Site 

identifier Location (ft3/s) (acre-ft/d)

1 Webb Ranch............. 2.7 (1) — na na na 2 Pier Street................. 3.7 (1) — na — 1.0 

LT Los Trancos Creek above confluence 

with San Francisquito Creek na (1) — na — na 

Below confluence2.... 3.7 — — na — na 

3 USGS stream gage 11164500 (Stanford 

Golf Course)........ 4.8 1.97 3.9 Fair — 1.1 

4 Sand Hill Road......... 5.4 (1) — na — .6 5 San Mateo Drive bike bridge 6.3 1.36 2.7 Fair 3 −1.2 .9 6 Alma Street .............. 7.4 5.07 .1 Good 6 −2.6 1.1 7 Middlefield Road ..... 8.1 .00 .0 na −.1 .7 8 1200 block of Woodland Avenue 9.1 5.19 .4 Good 6 +.4 1.0 9 University Avenue.... 9.7 .00 .0 na −.4 .6 
20 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

seepage runs. The average change in streamflow 

between sites 3 and 4 was a loss of 0.1 acre-ft/d for the 

four seepage runs. The measured gains in streamflow 

within this reach may have been due to ground-water 

underflow from the surrounding bedrock. As shown in 

figure 5 (A-A′), a bedrock assemblage is near the channel bottom west of the Pulgas Fault at site 4. Because 

water-level data were not available for the area west of 

the Pulgas Fault, the altitude of the water table in the 

bedrock could not be determined.

Losses in streamflow along San Francisquito 

Creek increased beginning between sites 4 and 5 

(fig. 7). Estimated losses between these sites averaged 

1.1 acre-ft/d for the five seepage runs (fig. 8). The 

greatest losses from San Francisquito Creek were along 

a 1.8-mile section of the creek between site 5 (San 

Mateo Drive bike bridge) and site 7 (Middlefield Road). 

Losses between sites 5 and 6 averaged 3.1 acre-ft/d for 

three seepage runs (April 29, 1996; February 25–27, 

1997; and April 30, 1997) and losses between sites 6 

Figure 7. Streamflow measurements for the five seepage runs along San Francisquito Creek, southern San Mateo and northern Santa Clara 

Counties, California.

Streambed materials

Seepage runs—Number is streamflow-

 measurement station identifier

 

Low-flow conditions

Intermediate/high-flow conditions

0

20

5

10

15

0 2 4 6 8 10 12

DISTANCE FROM SEARSVILLE LAKE, IN MILES

0

4

1

2

3

STREAMFLOW, IN CUBIC FEET PER SECOND

Unconsolidated alluvium

Partly consolidated and consolidated

 bedrock assemblages

Represents sum of flow at site 2 

 and inflow from Los Trancos 

 Creek except for July 22, 1996,

 seepage run when it represents

 sum of flow at site 1 and inflow

 from Los Trancos Creek

 

Represents sum of flow minus 

 flow from Stanford diversion 

 intake just upstream of site 3

+LT

-SD

1

1

1

2

2

1 2

+LT

+LT

+LT

+LT

-SD

-SD

3

3

3

3

3

4

4

4

4

5

5

5

5

6

6

6

7

7

7

8

8

8

8

9

9

9

10

10

10

A11

11

11

11

12

12

12

 April 29, 1996 

 June 13, 1996 

 July 22, 1996 

 April 30, 1997

 February 25-27, 1997

EXPLANATION
Measured Streamflow Gains and Losses 21 Figure 8. Average streamflow gains or losses by reach between sites 3 and 12 along San Francisquito Creek, southern San Mateo and northern Santa C

section modified from figure 5; refer to that figure for the explanation of this figure.)

ACRE-FEET/DAY

FEET

 Site 4 

Site 3 

Site 5 

Site 6 

Site 7

Site 8

Site 9

Site 10

Site 11

Site 12SW 

bottom

Channel

0

0

1

1

2 Kilomet

VERTICAL SCALE GREATLY EXAGGERATED

D-L D-L

S S

-9 est -2 est 22' 14' est 25'

? ? D-U

D-U

Hwy 101 

 Sea level

 300 200

 200

 100

 100

300

 400

 500

 600

5S/3W-34H1 

(projected)

5S/3W-35G10

5S/3W-36D1

 (projected)

5S/3W-36F2

6S/3W-3M10

6S/3W-3M2

? ?

A 

 -0.5

 -2.0

 -1.5

 0.5

 -1.0

 0

1.0

 -2.5

 -3.0

 -3.5

1.5 

Gain

Loss
22 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

and 7 averaged 2.5 acre-ft/d for two seepage runs 

(April 29, 1996, and February 25–27, 1997) (fig. 8). 

Streamflow losses were greatest between sites 5 and 7 

owing to the combination of predominantly 

course-grained alluvium and ground-water levels in 

nearby wells that were substantially (more than 20 ft) 

below the bottom of the channel. Because there are six 

large storm drains between sites 5 and 6, these estimated losses may be low. Because these storm drains 

were not checked during each seepage run, it is not 

known whether the measured losses between sites 5 

and 6 were masked by inflow.

Streamflow gains were measured between sites 7 

and the 1200 block of Woodland Avenue (site 8) for the 

four seepage runs for which measurements were made 

at both sites (tables 1, 2, 4, and 5); gains averaged 

0.8 acre-ft/d (fig. 8). The streamflow gains measured in 

this reach may be attributed to urban runoff. Two large 

storm drains discharge to San Francisquito Creek in 

this reach (fig. 2), but their discharge to the creek was 

not measured. The gain in streamflow may also be 

attributable to ground-water discharge to the stream 

channel. Water-level measurements from nearby wells 

indicate that the regional water table may coincide with 

the channel bottom along this reach of San Francisquito 

Creek (fig. 8), particularly during the winter and early 

spring when water levels usually reach their maximum.

Streamflow losses were measured between sites 

8 and site 9 (University Avenue) during the four 

seepage runs for which measurements were made at 

both sites (tables 1, 2, 4, and 5). Streamflow losses 

averaged 1.6 acre-ft/d (fig. 8) for the April 1996 and 

February 1997 seepage runs when flow was measurable 

at both sites. During the June 1996 and April 1997 

seepage runs, no streamflow was measured at site 9 

owing to the complete loss of flow between sites 8 and 

9. Losses measured during the June 1996 and April 

1997 seepage runs were not included in the calculated 

average loss because they represent losses for only a 

part of this reach.

Streamflow loss for the reach between sites 9 and 

site 10 (Newell Road) averaged 1.0 acre-ft/d (fig. 8) 

owing to a loss of 2.4 acre-ft/d during the high-flow 

seepage run of February 1997 and a slight gain of 

0.5 acre-ft/d during the seepage run of April 1996 

(tables 4 and 1, respectively). The streamflow gain of 

April 1996 probably was not from storm drains: there 

are no known storm drains contributing inflow from the 

city of East Palo Alto, which drains directly to San 

Francisco Bay (Mahendar Chima, city of East Palo 

Alto, oral commun., 1997), or from the city of Palo 

Alto. Furthermore, the streamflow gain probably was 

not from the shallow aquifer because the water table in 

this reach was at least 10 ft below the bottom of the 

channel owing to the presence of nearby production 

wells (fig. 8). It is possible that limited streamflow gains 

of a very localized nature originated from a perched 

zone of gravel overlying beds of clay or silt.

 Streamflow gains of 1.0 and 0.8 acre-ft/d 

measured between sites 10 and East Bayshore Road 

(site 11) during the April 1996 and February 1997 

seepage runs (tables 1 and 4, respectively) may be 

attributable to urban runoff. A large storm drain (at site 

A11 on figure 2) drains much of the city of Palo Alto. 

Measurements of discharge from this drain during the 

February 1997 seepage run indicate that this drain 

accounts for the entire streamflow gain of 0.8 acre-ft/d 

measured in the reach between sites 10 and 11 (table 4). 

The storm drain at site A11 also may be the source of 

the 1.0 acre-ft/d streamflow gain measured between 

sites 10 and 11 during the April 1996 seepage run, but 

the drain was not checked for flow during that seepage 

run. Streamflow losses in this reach probably are 

negligible because the water table is near the bottom of 

the channel (fig. 8).

A streamflow loss of 0.8 acre-ft/d was measured 

between sites 11 and the Palo Alto Municipal Golf 

Course (site 12) during the April 1996 seepage run, and 

a gain of 1.6 acre-ft/d was measured during the 

February 1997 seepage run (tables 1 and 4, 

respectively). The determination of streamflow gains 

and losses for this reach was difficult because of the 

probable influence of high tides as far upstream as site 

11. Additional seepage runs are needed to more 

accurately characterize the reach between sites 11 and 

12.

Estimated Ground-Water Recharge from San 

Francisquito Creek

To assess the importance of San Francisquito 

Creek as a source of water to area wells, its contribution 

to ground-water recharge was estimated using 

streamflow data from two sources: streamflow 

measurements from the 1996–97 seepage runs and 

historical streamflow records for USGS stream gage 

11164500 for water years 1932–41 and 1951–99. For 

this study, average annual recharge was estimated for 

the reaches between sites 3 and 12, with emphasis on 

the reaches between sites 5 and 7 where the greatest 

streamflow losses occurred.

Reaches upstream of site 3 were not included in 

the estimate of recharge from San Francisquito Creek. 

Site 3 roughly corresponds to the location where San 

Francisquito Creek crosses the contact between partly 

consolidated to consolidated rock and unconsolidated 

alluvium. It was assumed that streamflow losses within 
Measured Streamflow Gains and Losses 23

the upstream reaches, which are underlain by partly 

consolidated and consolidated rock, do not contribute 

to direct recharge of the alluvial fan but are lost to bank 

storage and localized channel deposits. Some portion of 

these upstream losses may contribute to recharge of the 

San Francisquito alluvial fan by subsurface inflow 

within the channel sediments.

The quantity of seepage that ultimately reaches 

and contributes recharge to the aquifer system was 

assumed to be reduced by evaporation from the water 

surface and transpiration by riparian plants along the 

channel. Previous studies on evapotranspiration 

indicate that water loss for vegetation similar to that 

found in the San Francisco Bay area generally is 

between 0.004 and 0.014 foot per day (ft/d) (Blaney 

and Muckel, 1955; Lull, 1964). For this study, 

evapotranspiration losses for the approximately 

33,250-foot length of stream channel between sites 3 

and 12 were estimated to be 150 acre-ft/yr assuming a 

uniform vegetation coverage, an average channel and 

riparian zone width of 60 ft, and an average 

evapotranspiration rate of 0.009 ft/d.

A three-step approach was used to estimate 

average annual recharge to ground water from each 

losing reach of San Francisquito Creek. First, the 

average daily streamflow loss for each losing reach was 

used to estimate the flow rate necessary at USGS stream 

gage 11164500 (site 3) to sustain flow through the 

entire downstream reach. For example, the average 

estimated daily streamflow loss between sites 3 and 4 is 

0.1 acre-ft/d, or 0.05 ft3

/s (table 6). To sustain flow 

throughout this reach, a rate of 0.05 ft3

/s was required at 

site 3. Similarly, the estimated average streamflow loss 

between sites 4 and 5 is 1.1 acre-ft/d, or 0.55 ft3

/s (table 

6). Therefore, to sustain flow between sites 3 and 5 a 

flow rate of 0.60 ft3

/s was necessary at site 3; this rate 

was calculated by adding the loss between sites 3 and 4 

and sites 4 and 5. For this additive approach, it was 

assumed that streamflow losses were distributed 

equally over the entire length of each losing reach.

Table 6. Estimated average streamflow gains and losses and estimated average annual streamflow loss, evapotranspiration loss, and 

ground-water recharge for reaches between sites 3 and 12 along San Francisquito Creek, southern San Mateo and northern Santa Clara 

Counties, California

[Reach refers to the section between two consecutive streamflow-measurement stations. See figure 2 for location of the sites. mi, mile; acre-ft/d, acrefoot/day; ft3

/s, cubic foot per second; acre-ft, acre-foot , —, no data] 

1 Average does not include losses measured on June 13, 1996, and July 22, 1996, because no flow was measured at site 6.

2 Average does not include loss measured on April 30, 1997, because no flow was measured at site 7.

3 Average does not include losses measured on June 13, 1996, and April 30, 1997, because no flow was measured at site 9.

4 Average may be due entirely to storm drain inflow at site A11.

Reach

Flow

distance 

between

stations

(mi)

Estimated

average

streamflow

gain/loss

(acre-ft/d) 

Estimated

average 

streamflow 

loss 

(ft3/s)

Minimum flow

needed at site 3

to maintain flow 

at bottom of

each reach

(ft3/s)

Estimated annual 

number of flow

days between

top and bottom

of each reach

Estimated 

annual

streamflow

loss

(acre-ft) 

Estimated 

annual

evapotranspiration loss

(acre-ft)

Estimated 

annual

ground-water

recharge

(acre-ft)

3–4 0.6 −0.1 −0.05 0.05 308 31 14 17

4–5 .9 −1.1 −.55 .60 167 184 22 162

5–6 1.1 1−3.1 −1.56 2.16 112 348 26 322

6–7 .7 2−2.5 −1.26 3.42 100 249 17 232

7–8 1.0 +0.8 — — — — 24 —

8–9 .6 3−1.6 −.81 4.23 93 149 14 135

9–10 .3 −1.0 −.50 4.73 90 90 7 83

10–11 .7 4+0.9 — — — — 17 —

11–12 .4 +0.4 — — — — 10 —

Total ...................................................................................................................... 1,051 151 951
24 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

For the second step, a flow-duration analysis was 

done to determine the number of days that sustainable 

flow might occur at downstream sites in relation to 

site 3. Flow-duration analysis involves ranking the 

magnitude and frequency of daily average streamflow 

recorded for a gaging station. This relation is best 

illustrated by a logarithmic plot called a flow-duration 

curve. The flow-duration curve for USGS stream gage 

11164500 shows the percentage of time that a 

particular streamflow value was equaled or exceeded 

during water years 1932–41 and 1951–99 (fig. 9). 

Interpolation of the flow-duration curve indicates that 

the minimum estimated flow rate at site 3 necessary to 

sustain flow at the bottom of each losing reach occurs 

from 84 percent of the time, or about 308 days annually, 

for the reach between sites 3 and 4, to about 25 percent 

of the time, or 90 days annually, for the reach between 

sites 9 and 10 (table 6).

As the final step, annual ground-water recharge 

was estimated for each losing reach between sites 3 and 

12 using the estimated annual number of flow days 

derived from the flow-duration curve and an estimated 

evapotranspiration rate of 150 acre-ft/yr. The daily 

average streamflow loss (table 6) was multiplied by the 

estimated annual number of flow days for each losing 

reach to give the annual streamflow loss for each reach. 

Evapotranspiration losses were proportioned for each 

Figure 9. Streamflow frequency for U.S. Geological Survey (USGS) stream gage 11164500 (site 3) on San Francisquito Creek, southern San 

Mateo and northern Santa Clara Counties, California, water years 1932–41 and 1951–99. (Discharge values in parentheses represent the 

mean streamflow during the time frame of each seepage run; ft3

/s cubic feet per second)

 DAILY MEAN STREAMFLOW, IN CUBIC FEET PER SECOND 

10,000

1,000

 100

10

1

0.1

0.13 0.5 1 2 5 10 20 30 40 50 60 70 80 90 95 98 99 99.5 99.87

*

**

*

*

*

*

*

*

*

*

*

*

*

*******

*

*

*

PERCENTAGE OF TIME INDICATED VALUE WAS EQUALED OR EXCEEDED

February 25-27, 1997 (21 ft3/s)

April 29, 1996 (6.5 ft3/s)

April 30, 1997 (2.7 ft3/s)

June 13, 1996 (1.2 ft3/s)

July 22, 1996 (0.98 ft3/s)
Characterization of Surface-Water and Ground-Water Quality 25

reach, whether losing or gaining, using the flow distance of each reach with respect to total flow distance 

between sites 3 and 12. Estimated evapotranspiration 

losses were subtracted from annual streamflow losses 

to calculate the annual ground-water recharge for those 

reaches of San Francisquito Creek that had streamflow 

losses (table 6).

Estimated average streamflow losses totaled 

approximately 1,050 acre-ft/yr for the reaches between 

sites 3 and 12, including approximately 595 acre-ft/yr 

for the 1.8-mile section between sites 5 and 7 (table 6). 

These estimated annual losses may be conservative 

because they do not include losses for those times when 

streamflow drys up between the measurement sites. 

High-flow conditions also may not be accurately 

represented by these estimated annual streamflow 

losses; during extended periods of high flow, average 

daily streamflow losses may increase owing to the 

submergence of more surface area along the 

streambanks and channel bottom. After accounting for 

evapotranspiration, estimated recharge to ground water 

from San Francisquito Creek totaled about 950 acre-ft 

during an average year (table 6), assuming that the five 

seepage runs represented the full range of streamflow 

conditions during an average year. This value 

represents only about 7 percent of the total mean annual 

flow at USGS stream gage 11164500 for water years 

1932–41 and 1951–99. About 58 percent, or 550 acreft, of the total estimated average annual recharge from 

San Francisquito Creek occurred between sites 5 and 7. 

Another approximately 19 percent, or about 

180 acre-ft/yr, of recharge from the creek occurred 

between sites 3 and 5. The remaining 23 percent, or 

about 220 acre-ft/yr, of recharge from the creek 

occurred downstream from site 7. The actual amount of 

recharge in the reaches downstream from site 7 may be 

higher than that estimated for this study. Streamflow 

gains between sites 7 and 8 and downstream from site 

10, which correspond with parts of the creek where the 

regional water table may coincide with the channel 

bottom, may have masked the actual quantity of 

recharge. If the water table was below the channel 

bottom part of the year, then the streamflow losses in 

those reaches may have exceeded the streamflow gains 

from ground water during that part of the year. 

CHARACTERIZATION OF SURFACE-WATER AND 

GROUND-WATER QUALITY

Water from San Francisquito Creek, Lake 

Lagunita, public supply, and the shallow and deep 

aquifers of the San Francisquito Creek alluvial fan were 

sampled for analysis of major ions, trace elements, 

silica, nutrients (appendix A), and the stable isotopes of 

oxygen (oxygen-18) and hydrogen (deuterium) 

(table 7). These data were used to help characterize the 

areal and vertical distribution of ground-water recharge 

from San Francisquito Creek to area wells. Samples 

were collected from sites along San Francisquito 

Creek, at Lake Lagunita, and at a residential tap 

receiving treated public municipal water. Ground-water 

samples were collected from wells located on both sides 

of, and at various distances from, San Francisquito 

Creek (fig. 10) and screened at various depths in the 

shallow and deep aquifers.

Methods of Water Sampling and Analysis

Surface-water samples were collected from San 

Francisquito Creek in April 1996, June 1996, and April 

1997. Samples collected at nine sites in April 1996 and 

at four sites in June 1996 were analyzed for stable 

isotopes of oxygen (18O) and hydrogen (2

H, deuterium). 

Samples collected at four sites in April 1997 were 

analyzed for major ions, trace elements (boron, 

bromide, iodide, iron, and manganese), silica, nutrients, 

and stable isotopes of oxygen and hydrogen. Most of 

the samples collected in April and June 1996 were 

measured on site for specific conductance and water 

temperature. Samples collected in April 1997 were 

measured on site for specific conductance, pH, water 

temperature, and alkalinity following procedures 

outlined by Ward and Harr (1990).

The one sample of Lake Lagunita water was 

collected approximately 40 ft from the northeast bank 

of the lake; it was analyzed for the same constituents as 

the other surface-water samples collected in April 1997. 

Lake Lagunita was sampled because it is a source of 

ground-water recharge to the shallow and deep aquifers 

during the late winter and spring months when it holds 

a combination of runoff from the surrounding hills and 

water diverted from San Francisquito Creek.

The one sample of treated public supply water 

(imported water from the Hetch Hetchy Aqueduct) was 

collected in April 1997 from a residential tap in Palo 

Alto; this sample was analyzed for major ions, trace 

elements, silica, nutrients, and the stable isotopes of 

oxygen and hydrogen. Because treated public supply 

water is the predominant source of water for 

landscaping use in the study area, this water was 

analyzed to determine whether the treated water might 

be a source of recharge to ground water.

One additional stream sample was collected from 

a miscellaneous site (ADO) on the Arroyo Ojo de Agua 

and analyzed for the stable isotopes of oxygen and 

hydrogen (table 7) for comparison with water from San 
26 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Table 7. Summary of oxygen-18 and deuterium ratios in samples from ground-water wells, streamflow-measurement stations, Lake 

Lagunita, and public supply, southern San Mateo and northern Santa Clara Counties, California, 1996–97

[See figure 10 for location of wells and figure 2 for location of streamflow-measurement stations. USGS (U.S. Geological Survey) identification No. consists 

of latitude, longitude, and sequence number. Flow-condition rating (based on instantaneous streamflow at USGS stream gage 11164500): I, intermediate 

flow; L, low flow. ft3/s, cubic foot per second; per mil, parts per thousand.]

1

Water-quality sampling site (Arroyo Ojo de Agua).

2

Sample collected approximately 400 feet upstream of site 6 on indicated date.

3

Imported water from Hetch Hetchy aqueduct collected at a residential tap in Palo Alto.

State well No. 

or 

site identifier

(source of sample)

USGS 

identification No.

Sample

date

Instantaneous 

streamflow 

(ft3/s)

Flow-condition 

rating

Delta

oxygen-18

(per mil)

Delta

deuterium

(per mil)

Streamflow-measurement stations

Site ADO1 372725122144201 4-30-96 — –6.55 –45.4

Site 1 372426122120301 4-29-96

6-12-96

6.46

1.66

I

L

–5.32

–4.92

–33.4

–31.6

Site LT 372447122112701 4-29-96 1.83 I –5.53 –36.7

Site 3 372524122111801 4-29-96

6-12-96

4-30-97

6.62

1.18

1.97

I

L

L

–5.32

–5.12

–4.88

–33.4

–32.9

–34.5

Site 5 372622122104401 4-29-96

6-12-96

4-30-97

5.96

.26

1.36

I

L

L

–5.35

–4.99

–4.93

–34.5

–33

–33.4

Site 6 372651122100401 2

372651122100901 

4-29-96

4-30-97

3.83

.07

I

L

–5.37

–6.74

–32.8

–50.3

Site 8 372727122090001 4-29-96

6-12-96

4-30-97

2.52

.28

.19

I

L

L

–5.76

–6.59

–6.39

–37.2

–44

–43.3

Site 9 372726122082401 4-29-96 1.90 I –5.67 –36.9

Site 11 372713122073401 4-29-96 2.64 I –5.66 –37

Site 12 372719122071501 4-29-96 2.20 I –5.53 –36.3

Lake Lagunita and public supply

Lake Lagunita 372523122102401 4-30-97 — –3.7 –29.1

Public supply3 4-28-97 — –13.02 –96

Well sites

5S/3W-25F1 372818122082801 5-02-97 –7.23 –49.6

5S/3W-25G1 372809122081501 5-01-97 –6.58 –45.3

5S/3W-27G1 372809122102101 4-29-97 –8.14 –59.6

5S/3W-27K2 372756122102501 4-29-97 –6.78 –46.7

5S/3W-27R3 372747122100701 4-29-97 –7.12 –48.4

5S/3W-34H1 372722122100501 5-01-97 –6.44 –43.5

5S/3W-35D3 372738122100401 4-29-97 –6.65 –45.8

5S/3W-35G10 372720122091501 5-01-97 –6.52 –43.8

5S/3W-36D1 372733122085701 5-02-97 –6.16 –41.8

5S/3W-36F2 372727122084001 4-28-97 –6.1 –41.6

5S/3W-36L10 372703122083201 4-28-97 –8.97 –66.4

6S/3W-1B2 372640122082401 5-01-97 –6.32 –43.2

6S/3W-1G1 372625122081301 4-28-97 –7.48 –53.6

6S/3W-2H10 372631122091001 4-28-97 –6.02 –40.8

6S/3W-3M2 372620122105601 5-01-97 –5.39 –38.2

6S/3W-3M10 372616122105301 5-02-97 –6.01 –42.9

6S/3W-11B10 372545122092001 5-02-97 –5.81 –40.8
Characterization of Surface-Water and Ground-Water Quality 27

Figure 10. Locations of ground-water, surface-water, and miscellaneous water-chemistry sampling sites, southern San Mateo and northern 

Santa Clara Counties, California.

Woodside 

 

 Rd

El Camino Real

El Camino Real

Middlefield 

Middlefield 

 Lake 

Lagunita

Bear Gulch 

Reservoir

Embarcadero Embarcadero 

Alma 

 St



Page Mill Rd

 STANFORD 

GOLF COURSE

 WEBB RANCH

 (Stanford)

Sand Hill Rd

El Camino

Real

Foothill

Exprwy

Arestradero

Rd

Bayshore

Bayshore

Freeway

Freeway

Rd

 PALO ALTO

 MUNICIPAL

GOLF COURSE

Charleston Rd

 Rd

San Antonio

Rd

Searsville

Lake

Junipero

Serra

Freeway

Sand 

Hill

Rd

Mt

Home Rd

Alpine Rd

Junipero Serra

Blvd

Santa Cruz Ave

Alpine Rd

San Francisquito

Creek

Los Trancos Cr

Marsh Rd

Atherton 

 

Ave

Alameda de las 

Woodside Rd

Whiskey Hill Rd

Stanford 

Ave

Jefferson

Ave

Bay

Bay

Rd

Rd

Whipple

Ave

El Camino

 Road

Far m

Hill Blv

Cr

Redwood

Creek

Arro yo Ojo de Ag ua

University

Ave

Matadero

Creek

Deer Cr

Barron 

Real

Atherton

Channel

Rd

Rd

Cordilleras

37°

30'

T 5 S

T 6 S

37°

27'

30"

37°

25'

0

0

1

1

2

2

3 Miles

3 Kilometers

Ravenswood Point

Creek

Pulgas

Adobe Creek

Newell

HETCH HETCHY

HETCH HETCHY

AQUEDUCT

AQUEDUCT

























 

 





1

2

3

4

11164500

11164500

LT

4

5

7 8 9

10

6

11

12

LL

LL

ADO

Sand Point

Rd

Dumbarton Bridge

Willow

Willow 

 Rd

Ringwood Ave

Middlefield 

 Road

University Ave

Ravenswood 

City Hall

City Hall

City Hall

Stanford University

SALT EVAPORATORS SALT EVAPORATORS

SALT EVAPORATORS

SALT EVAPORATORS

 SALT 

 EVAPORATORS

Redwood City

Atherton

Menlo Park

Palo Alto

 East

 Palo Alto

San Francisco Bay

Bayfront Expwy

Ave

Hamilton

Chilco St

82

122°15' R 4 W R 3 W 122°12'30" 122°10' R 3 W 122°07'30" R 2 W

Base from U.S. Geological Survey

1:24,000 Palo Alto, 1991

27G1

27R3

35D3

34H1

3M2

3M10

36D1

35G10

36D1

36F2

36L10

1B2

2H10

1G1

11B10

3M2

3M10

25F1

25G1

Temporary streamflow-measurement station and station identifier

Well and number—Abbreviated number does not include township and range designations 

 (see "well-numbering system")

Miscellaneous water-chemistry samping site and site identifier

EXPLANATION

Contact between partly consolidated and consolidated bedrock assemblages (hachured side)

 and unconsolidated alluvium—Modified from Fio and Leighton (1995)

3

Shallow aquifer

Deep aquifer–upper zone

Deep aquifer–lower zone

84

San

Francisquito

Creek

27K2

San Mateo Dr

Woodland Ave

E. Bayshore Rd E. Bayshore Rd

Pier St

280

101

Stream-gaging station and identifier (11164500) and temporary site identifier (3)—Site 3 is 

 a temporary streamflow measurement station adjacent to permanent stream-gaging station 
28 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Francisquito Creek. Arroyo Ojo de Agua is located 

near Redwood City in the Redwood Creek drainage 

basin northwest of San Francisquito Creek (fig. 10).

Ground-water samples were collected from 

17 wells in late April and early May 1997: 7 wells were 

screened in the shallow aquifer, 5 wells were screened 

in the upper zone of the deep aquifer, and 5 wells were 

screened in the lower zone of the deep aquifer (table 8). 

These samples were collected from a faucet either at or 

near the well head to minimize potential chemical 

alteration of the water between the well and the 

sampling point. The samples were analyzed for major 

ions, selected trace elements, silica, nutrients 

(appendix A), and the stable isotopes of oxygen and 

hydrogen (table 7). Selection of wells was based on 

accessibility, average depth of the perforated interval 

(well screen), and proximity of a well to other wells 

selected for water-chemistry sampling and to San 

Francisquito Creek. Wells in the shallow aquifer were 

paired with wells in the deep aquifer whenever feasible 

to assess variation in water chemistry with depth.

Prior to the collection of the ground-water 

samples, the wells were purged of a minimum of three 

casing volumes of water. Sequential measurements of 

specific conductance, pH, and temperature were made 

at 5-minute intervals until readings had stabilized to 

ensure the representativeness of the ground-water 

samples. All samples were collected, treated, and 

preserved following procedures outlined by Ward and 

Harr (1990). Major ions, trace elements, silica, and 

nutrients were analyzed at the USGS National Water 

Quality Laboratory at Arvada, Colorado, using standard 

analytical methods described by Fishman and Friedman 

(1989), Fishman (1993), and Struzeski and others 

(1996). Stable isotopes of oxygen and hydrogen were 

analyzed by the USGS Isotope Fractionation Project at 

Reston, Virginia, using a hydrogen-water-equilibration 

technique (Coplen and others, 1991).

The variation of major-ion concentrations in 

surface- and ground-water samples was assessed using 

a trilinear diagram. A trilinear diagram shows the 

proportions of common cations and anions for 

Table 8. Construction data, depth to partly consolidated and consolidated bedrock assemblages, and aquifer zone of ground-water wells 

used for water-chemistry sampling in southern San Mateo and northern Santa Clara Counties, California

[See figure 10 for well locations. State well No., see “Well-Numbering System” section in the text. USGS (U.S. Geological Survey) identification No. consists 

of latitude, longitude, and sequence number. Depths in feet below land surface. Depth to partly consolidated and consolidated bedrock assemblages from 

Carle and others (1990). Elevation of land surface in feet above sea level. Aquifer zones: shallow, 15 to 100 feet below land surface; deep-upper, 200 to 300 

feet below land surface; and deep-lower, greater than 300 feet below land surface (all depths are approximate). Aquifer zone perforated based on center of 

depth of perforated interval. ≈, where approximated/interpolated]

State well No. USGS

identification No.

Depth of

well boring

Completed well 

depth

Depth of

perforated

interval

Depth to partly

consolidated and 

consolidated

bedrock assemblages

Elevation

of land

surface

Aquifer zone 

perforated

5S/3W-25F1 372818122082801 351 334 258–323 ≈1,055 19 Deep-lower

5S/3W-25G1 372809122081501 54 54 31–48 ≈1,120 15 Shallow

5S/3W-27G1 372809122102101 65 58 38–58 ≈410 35 Shallow

5S/3W-27K2 372756122102501 300 290 145–280 ≈375 45 Deep-upper

5S/3W-27R3 372747122100701 163 160 28–140 ≈525 46 Shallow

5S/3W-34H1 372722122100501 310 290 180–270 667 53 Deep-upper

5S/3W-35D3 372738122100401 435 425 160–420 ≈620 50 Deep-upper

5S/3W-35G10 372720122091501 935 840 108–822 ≈880 44 Deep-lower

5S/3W-36D1 372733122085701 608 550 181–532 ≈1,100 38 Deep-lower

5S/3W-36F2 372727122084001 260 260 150–260 ≈1,210 36 Deep-upper

5S/3W-36L10 372703122083201 65? 65 20?–65? ≈1,150 23 Shallow

6S/3W-1B2 372640122082401 1,082 900 150–882 ≈1,125 24 Deep-lower

6S/3W-1G1 372625122081301 72 72 53–64 ≈1,200 19 Shallow

6S/3W-2H10 372631122091001 85? 85 20?–85? ≈730 40 Shallow

6S/3W-3M2 372620122105601 100 100 20–80 ≈500 87 Shallow

6S/3W-3M10 372616122105301 320 301 142–301 ≈510 93 Deep-upper

6S/3W-11B10 372545122092001 828 624 144–624 454 51 Deep-lower
Characterization of Surface-Water and Ground-Water Quality 29

comparison and classification of water samples independent of total analyte concentrations (Hem, 1985). 

Water samples having the same composition, but different total concentrations, will plot at the same location on a trilinear diagram. This diagram permits the 

compositions of many samples to be shown on the 

same graph enabling major groupings or trends to be 

discerned visually (Freeze and Cherry, 1979).

Selected trace-element data were evaluated to 

determine whether bay water is a contributing source of 

water to wells in the study area. Previous studies of 

coastal aquifer systems in California have used 

trace-element data to distinguish mixtures of native 

fresh water and seawater from mixtures of native fresh 

water and high chloride water from other sources such 

as brines from underlying or surrounding rocks, 

estuarine deposits, and surface contamination (Piper 

and others, 1953; Martin, 1984; and Izbicki, 1991). For 

this study, ratios of chloride to boron, bromide, and 

iodide, relative to the concentration of chloride, were 

plotted to show the relation between ground water and 

seawater. Ratios are presented on a millimole per 

millimole basis, rather than on a mass per mass basis, 

so that ratios calculated from different trace elements, 

each having different atomic masses, are comparable. 

Chloride and trace-element concentrations listed in 

appendix A were converted from mass per unit volume 

[milligrams per liter (mg/L)] to millimoles (mmol) per 

unit volume by dividing by the atomic weight of each 

constituent. For example, to convert the chloride 

concentration for seawater to millimoles, 19,000 mg/L 

(Hem, 1985) was divided by the atomic weight of 

chloride (35.4 milligrams (mg) in a millimole of Cl 

atoms) to get 536 millimoles per liter (mmol/L).

Major Ions

Surface Water

In general, the dissolved-solids concentration of 

San Francisquito Creek varies as a function of seasonal 

changes in hydrologic conditions. During periods of 

dry weather when streamflow is low, the dissolved 

solids tend to be high; during periods of wet weather, 

they tend to be low owing to dilution by surface runoff. 

This inverse relation between dissolved solids and 

streamflow can be illustrated by specific conductance. 

Specific conductance is the ability of water to conduct 

an electric current; it provides an indication of the 

dissolved-solids concentration of water—the higher the 

electric current, the greater the dissolved-solids 

concentration (Hem, 1985). Specific conductance 

measurements made at the streamflow stations along 

San Francisquito Creek in 1996 and 1997 ranged 

between 870 and 1,270 microsiemens per centimeter 

(μS/cm) in the samples collected from sites upstream of 

site 6 during the low-flow seepage runs and between 

730 and 801 μS/cm in all the samples collected during 

high-flow seepage runs (appendix A). Several samples 

collected during the low-flow seepage runs at sites 6 

and 8 had lower specific conductance than the upstream 

samples. The lower specific conductance values of the 

samples collected from site 8 in June 1996 (770 μS/cm) 

and from sites 6 and 8 in April 1997 (580 and 

754 μS/cm, respectively) indicate that during low-flow 

conditions water downstream from site 5 is not solely 

streamflow from the upper reaches of San Francisquito 

Creek. Urban runoff of imported water, the principal 

source of supply for residential irrigation and other 

domestic uses in the study area, is an additional source 

of streamflow downstream from site 5. Because 

imported water has a much lower dissolved-solids 

concentration [a specific conductance of 77 μS/cm in 

the sample collected from a residential tap in April 

1997, and an average specific conductance of 

124 μS/cm reported for treated imported water in 1997 

(San Francisco Public Utilities Commission, electronic 

data, accessed 2001)] than water from San Francisquito 

Creek, mixing of these two waters lowers the dissolvedsolids concentration of San Francisquito Creek 

downstream from site 5 during low-flow conditions.

Major-ion concentrations were analyzed in 

samples collected at sites 3, 5, 6, and 8 along San 

Francisquito Creek during April 1997 (appendix A). 

The concentrations in these samples, however, may not 

be representative of average conditions because the 

samples were collected during a period of dry weather 

and low streamflow. Samples from Lake Lagunita and 

from a residential tap (imported water) also were 

analyzed (appendix A). These samples have a mixed 

chemical composition and plot in the same general area 

on the trilinear diagram (fig. 11). In general, calcium 

and magnesium are the predominate cations, and 

carbonate and bicarbonate are the predominate anions 

in the surface-water samples (fig. 11). The proportions 

of cations and anions in these samples reflect the 

original composition of the source water and changes in 

its composition owing to contact and residence time 

with various geologic materials, biological processes, 

and mixing with water from local and imported sources.

These chemical analyses provide additional 

evidence that the samples collected from sites 6 and 8 

during the low-flow conditions of April 1997 were 

diluted by urban runoff. Concentrations of magnesium, 

sodium, sulfate, chloride, boron, and total dissolved 

solids were lower in samples from sites 6 and 8 than in 

samples from upstream sites 3 and 5 (appendix A). 
30 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Figure 11. Chemical composition of water from selected ground-water wells, streamflow-measurement stations, Lake Lagunita, and public 

supply, southern San Mateo and northern Santa Clara Counties, California, April 28 through May 2, 1997.

Group 2

Group 3

Group 1

 Ground water from deep-upper aquifer well

 Ground water from shallow aquifer well

 Group 1: Samples similar to composition of surface water

 Group 2: Samples from shallow aquifer wells with increasing bicarbonate and 

 decreasing sulfate concentrations

 Group 3: Samples from deep aquifer wells affected by cation exchange and

 increasing chloride concentrations

 Ground-water sample data groups:

20

40

60

80

20

40

60

80

80

60

40

20

80

60

40

20

20

40

60

80

80

60

40

20

80

60

40

20

20

40

60

80

80 60 40 20 20 40 60 80

Magnesium

Sulfate

Sodium + Potassium

Carbonate + Bicarbonate

Sulfate + Chloride

Calcium Chloride 

C A T I O N S A N I O N S

 Ground water from deep-lower aquifer well

 Surface water from San Francisquito Creek

 Imported (public supply) water from residential tap

 Surface water from Lake Lagunita

EXPLANATION

San Francisco Bay water (Iwamura, 1980)

Calcium + Magnesium

36D1

36F2

1B2

25F1

27K2

35G10

11B10

35D3

36D1

1G1 36L10

2H10

27R3 27G1

Site 8

Site 5

Site 6

Site 3

 Example of how to read a trilinear diagram for sample from site 8

25G1

3M10

3M2

PERCENTAGE OF TOTAL MILLIEQUIVALENTS PER LITER





 



   













 Bay 

water Lake

Lagunita

 public

 supply 34H1







Characterization of Surface-Water and Ground-Water Quality 31

Despite higher flow rates at the upstream sites in 

relation to the downstream sites, total dissolved-solids 

concentrations were higher in the samples from sites 3 

(563 mg/L) and 5 (591 mg/L) than in the samples from 

sites 6 (327 mg/L) and 8 (447 mg/L). In contrast, 

phosphorus, a component of some detergents, was 

0.06 mg/L in the sample from site 6, which is about 

twice the average concentration of phosphorus in 

samples from sites 3, 5, and 8. Nitrite plus nitrate as 

nitrogen was lower in the sample from site 6 

(0.32 mg/L) relative to the other samples from San 

Francisquito Creek, but higher in the sample from site 8 

(2.2 mg/L). The higher nitrogen concentration in the 

sample from site 8 suggests that urban runoff at this site 

may have included fertilizers containing nitrogen.

Ground Water

The results of ground-water sampling and 

analyses indicate a wide variation in the chemical 

composition of ground water in the study area. Use of 

this data to help characterize the areal and vertical 

distribution of the ground-water quality of the 

San Francisquito Creek area was limited, however, 

because the samples were collected from existing 

production wells, which in many cases are perforated in 

more than one aquifer. The ground-water samples from 

wells perforated in more than one aquifer may be 

representative of composite rather than aquifer-specific 

conditions. Despite these limitations, the analyses 

indicate spatial and depth-dependent differences in the 

composition of ground water.

Overall, the specific conductance of water from 

all wells sampled ranged from 678 μS/cm for the 

sample from well 5S/3W-36F2 to 1,740 μS/cm for the 

sample from well 5S/3W-27G1 (appendix A). The 

composition of ground water appears to vary primarily 

as a function of aquifer depth. The composition of 

ground water changes from a calcium-bicarbonate or 

mixed cation-bicarbonate water in the shallow aquifer 

(similar to the composition of surface water samples) to 

a sodium-chloride or mixed cation-mixed anion water 

in the lower zone of the deep aquifer (fig. 11). The 

composition of ground water from the upper zone of the 

deep aquifer does not appear to be dominated by any 

particular water type but instead consists of various 

combinations of the same cations and anions present in 

ground water from the shallow aquifer and lower zone 

of the deep aquifer.

The chemical composition of the ground-water 

samples collected and analyzed for this study plot 

within three distinct groups on the central diamond of 

the trilinear diagram (fig. 11). Samples from wells with 

a chemical composition most similar to that of surface 

water from San Francisquito Creek and Lake Lagunita 

plot within the circle labeled group 1. The wells within 

this group include three wells perforated in the shallow 

aquifer and one well perforated in the upper zone of the 

deep aquifer (6S/3W-3M10) located adjacent to a 

significant losing reach of San Francisquito Creek. 

Samples from wells that plot within the circle labeled 

group 2 are from four wells perforated in the shallow 

aquifer and from one well perforated in the upper zone 

of the deep aquifer (5S/3W-36F2) located adjacent to a 

losing reach of San Francisquito Creek. These samples 

are characterized by generally higher percentages of 

bicarbonate and lower percentages of sulfate and 

chloride than the samples within group 1. Ground-water 

samples that plot within the circle labeled group 3 are 

from wells in both the upper and lower zones of the 

deep aquifer. These samples are characterized by higher 

percentages of chloride and sodium and lower 

percentages of calcium, magnesium, and bicarbonate 

than the samples from group 1 or group 2.

The relation between water chemistry and 

aquifer depth may be attributed to natural systemic 

changes in the composition of water as it moves through 

different geologic materials. The similarity between the 

surface-water samples and the well samples from the 

shallow aquifer (fig.11) indicates that the surface water 

that recharges the underlying shallow ground water has 

had minimal residence time during which major 

changes in composition can occur. As water continues 

to migrate both downgradient through the alluvial fan 

towards San Francisquito Bay and vertically towards 

the deep aquifer, it encounters additional sediments in 

the aquifer where change in chemical composition can 

occur. Ground water that encounters clay-bearing 

aquifer deposits can be modified by cation exchange; 

for example, sodium cations on the clay minerals are 

replaced by calcium and magnesium cations, releasing 

the sodium cations to water (Drever, 1982). Cation 

exchange and the resulting contrast in water 

composition between the shallow and deep aquifers is 

most pronounced where the aquifers are separated by 

extensive deposits of bay mud and clay. This generally 

occurs throughout the lower part of the alluvial fan 

downstream from site 6 on San Francisquito Creek (for 

example, in water from wells 6S/3W-1G1 and 

6S/3W-1B2). Upstream of site 6, and perhaps along 

some downstream losing reaches of San Francisquito 

Creek, clay deposits are minimal or nonexistent. In 

these areas, the differences in ground-water 

composition between the shallow and deep aquifer are 

much less pronounced, as evidenced by the similar 

composition of the samples from wells 6S/3W-3M2 and 

6S/3W-3M10 (fig. 11).
32 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Samples from seven of the wells had chloride 

concentrations in excess of 100 mg/L (appendix A). 

Results of previous investigations in the study area 

indicate that bay water intrusion may be the source of 

the elevated chloride concentration in water from some 

area wells (Tolman and Poland, 1940; Iwamura, 1980). 

Trace-element data (boron, bromide, and iodide) from 

ground-water samples collected as part of this study 

were used to help determine the source of the elevated 

chloride concentration. Chloride-to-boron, chloride-tobromide, and chloride-to-iodide ratios were plotted as a 

function of chloride concentration to show potential 

mixing with bay water (fig. 12).

Boron concentration in the samples from wells 

collected for this study range from 170 to 660 μg/L 

with the highest concentration in the sample from well 

5S/3W-27K2 (appendix A). The boron concentration in 

seawater is 4,600 μg/L (Hem, 1985) and the 

concentration in bay water is 3,800 μg/L (Iwamura, 

1980). The samples with high chloride concentrations, 

except those from wells 5S/3W-25F1 and 6S/3W11B10, all plot below the mixing line between seawater 

and representative water from the shallow and deep 

aquifer systems (fig. 12A). The samples below the 

seawater mixing line are enriched with boron, possibly 

owing to leakage of ground water from the underlying 

partly consolidated to consolidated bedrock 

assemblages. The samples from wells 5S/3W-25F1 and 

6S/3W-11B10 plot slightly above the seawater mixing 

line. The source of the elevated chloride concentrations 

in water from these two wells cannot be definitively 

determined on the basis of boron concentrations.

 Bromide concentrations in the ground-water 

samples ranged from 0.11 to 0.98 mg/L; the highest 

concentration was in the sample from well 5S/3W-25F1 

(appendix A). In comparison, seawater has a bromide 

concentration of about 65 mg/L (Hem, 1985). 

Chloride-to-bromide ratios for all the ground-water 

samples plot within a narrow range and close to the 

ratio for seawater of 660 (fig. 12B). The chloride-tobromide ratio gradually increases as the chloride 

concentration increases and as water moves through the 

aquifer system; the ratio increases from an average of 

597 for water from the shallow and deep wells in the 

vicinity of losing reaches of San Francisquito Creek to 

an average ratio of 717 for the deep wells in other parts 

of the study area. The chloride-to-bromide ratios for 

most of the samples with a high chloride concentration 

exceed the ratio for seawater; however, the ratios of 

chloride-to-bromide were difficult to interpret because 

the values for ground water and seawater are similar.

Among the trace elements presented in this 

evaluation, iodide may be the most useful indicator for 

distinguishing between modern bay water intrusion and 

saline water from other sources, such as marine 

sediments. The concentration of iodide in seawater is 

only 0.06 mg/L (Hem, 1985), but iodide concentrations 

in ground water may be much higher, especially in 

water that has traveled through estuarine muds or that 

has had a long residence time in sedimentary deposits 

of marine origin (Lloyd, 1982). Iodide concentrations 

in ground-water samples ranged from 0.003 mg/L for 

wells 5S/3W-27G1and 36L10 and well 6S/3W-3M10 to 

0.601 mg/L for well 5S/3W-25F1. The samples from 

the shallow aquifer that had high chloride 

concentrations do not plot along the mixing line 

between seawater and a representative sample from the 

shallow aquifer (6S/3W-3M2) (fig. 12C). All the 

samples from the wells in the deep aquifer that had high 

chloride concentrations, except the sample from well 

6S/3W-11B10, plot below the mixing line between 

seawater and a representative sample from the deep 

aquifer (5S/3W-36D1). These samples are enriched 

with iodide, possibly from the dissolution of salts 

present in marine deposits. The sample from well 

6S/3W-11B10 plots above the seawater mixing line. 

The fact that this well is more than 3 mi from San 

Francisco Bay precludes bay water intrusion as the 

source of chloride to water from this well.

Analyses of trace-element data, especially 

chloride-to-iodide ratios, indicate that modern bay 

water intrusion is not the source of high chloride 

concentrations (greater than 100 mg/L) in water from 

wells sampled for this study. As water moves through 

the aquifer it may come in contact with chloride-rich 

marine sediments (undifferentiated clay) associated 

with bay deposits that overlay the shallow aquifer near 

San Francisco Bay and separate the shallow and deep 

aquifers throughout most of the study area (fig. 5). 

Marine sediments also are present in the partly 

consolidated to consolidated bedrock assemblages that 

underlay the deep aquifer. Mineral dissolution of these 
Characterization of Surface-Water and Ground-Water Quality 33

Figure 12. Selected trace-element ratios as a function of chloride concentration in water from wells, southern San Mateo and northern 

Santa Clara Counties, California, April 28 through May 2, 1997. A, chloride-to-boron. B, chloride-to-bromide. C, chloride-to-iodide.

0.1 1 10 100 1,000 10,000

1

10

100

1,000

10,000

100,000 10 100 1,000 10,000 100,000

Seawater (Hem, 1985)

Ground water from shallow aquifer well

 Deep aquifer—upper zone

Deep aquifer—lower zone

San Francisco Bay water (Iwamura, 1980)

25F1

25G1

27G1

27K2 27R3

34H1

35D3

35G10

36D1

36F2

1G1

1B2

36L10

2H10

3M2 3M10

11B10

0.1 1 10 100 1,000 10,000

100

1,000

10,000

100,000

1,000,000

10,000,000 10 100 1,000 10,000 100,000

25F1

25G1

27G1

27K2

27R3

34H1

35D3

35G10

36D1

36F2

1G1

1B2

36L10

2H10

3M2

3M10

11B10

0.1 1 10 100 1,000 10,000

1

10

100

1,000

10,000

100,000 10 100 1,000 10,000 100,000

25F1

25G1

27G1

27K2

27R3

34H1

35D3

35G10

36D1

36F2

1G1

1B2

36L10

2H10

3M2

3M10

11B10

CHLORIDE-TO-IODIDE RATIO, IN MILLIMOLES PER MILLIMOLE

CHLORIDE-TO-BROMIDE RATIO, IN MILLIMOLES PER MILLIMOLE

CHLORIDE-TO-BORON RATIO, IN MILLIMOLES PER MILLIMOLE

CHLORIDE, IN MILLIMOLES PER LITER

CHLORIDE, IN MILLIMOLES PER LITER CHLORIDE, IN MILLIMOLES PER LITER

CHLORIDE, IN MILLIGRAMS PER LITER

CHLORIDE, IN MILLIGRAMS PER LITER CHLORIDE, IN MILLIGRAMS PER LITER

EXPLANATION

deep aquifer wells

Most of shallow wells plus

one deep well near a losing reach

of San Francisquito Creek

Most of shallow wells plus

deep wells near losing reaches

of San Francisquito Creek

Most of shallow wells plus

deep wells near losing reaches

of San Francisquito Creek

C

A B

Seawater mixing line
34 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

marine sediments is probably the source of the high 

chloride concentration in water from wells sampled for 

this study.

Oxygen-18 and Deuterium

Oxygen-18 (18O) and deuterium (2H) are 

naturally occurring stable isotopes of oxygen and 

hydrogen. The abundance of oxygen-18 and deuterium 

relative to lighter oxygen-16 (16O) and hydrogen (1

H) 

atoms can be used to help infer the source and the 

evaporative history of water. Oxygen-18 and deuterium 

abundances are expressed in delta notation (δ) as per 

mil [parts per thousand (‰)] differences in the ratios of 

18O/16O and 2

H/1H in samples relative to a standard 

known as Vienna Standard Mean Ocean Water 

(VSMOW) (Gat and Gonfiantini, 1981):

and

Because the source of much of the world’s 

precipitation is derived from the evaporation of 

seawater, the δ18O and δD composition of precipitation 

throughout the world cluster along a line known as the 

global meteoric water line (Craig, 1961)

δD = 8δ18O + 10.

Water that has not undergone evaporation will 

plot near the global meteoric water line, whereas water 

that has undergone evaporation will plot to the right of 

the global meteoric water line towards less negative 

δ18O and δD.

The δ18O and δD values in water sampled from 

selected sites on San Francisquito Creek and Lake 

Lagunita and from public supply and selected 

production wells ranged from −3.7 to −13.02 per mil 

and −29.1 to −96 per mil, respectively (table 7). Except 

for one sample collected from San Francisquito Creek 

at site 6, these values plot below, but parallel to, the 

δ O 18

O 18 O 16 ⁄    

sample

O 18 O 16 ⁄     VSMOW

= ----------------------------------------------------- – 1 × 1 0, 00

δD

H

2 H1

⁄  

 

sample

H

2 H1

⁄  

 

VSMOW

= --------------------------------------------------- – 1 × 1 0, 00.

global meteoric water line along a line known as the 

local meteoric water line (fig. 13A). Evaporated waters 

plot farther to the right along a line referred to as the 

evaporative trend line (Gat and Gonfiantini, 1981); the 

sample from Lake Lagunita is partly evaporated and, 

thus, has the isotopically heaviest (least negative) water 

(δ18O and δD values of −3.7 and −29.1 per mil, 

respectively). Public supply water, which consists of 

surface water imported from the Hetch Hetchy 

Reservoir in the Sierra Nevada, was the isotopically 

lightest (most negative) water sampled (δ18O and δD

values of −13.02 and −96, respectively). The water 

imported from the Sierra Nevada is isotopically distinct 

from other waters in the study area because, as storms 

move inland from coastal areas, the concentration of 

heavier isotopes relative to lighter isotopes decreases as 

water molecules repeatedly undergo evaporation and 

condensation. Additionally, precipitation that 

condenses at higher altitudes and at cooler temperatures 

tends to be isotopically lighter than precipitation that 

forms at lower altitudes and warmer temperatures (Muir 

and Coplen, 1981). The latitude at which a storm 

originates can also affect the isotopic composition of 

precipitation (Gat and Gonfiantini, 1981); storms that 

originate over the cold waters of the Gulf of Alaska 

have a lighter isotopic composition than storms that 

originate over warm tropical waters in the vicinity of 

Hawaii.

The δ18O and δD composition of the streamwater samples from San Francisquito Creek and Arroyo 

Ojo de Agua (ADO) ranged from −4.88 to −6.74 per mil 

for δ18O and from −31.6 to −50.3 per mil for δD

(fig. 13B, table 7). With the exception of the samples 

from San Francisquito Creek at sites 6 and 8, the stream 

samples collected during low flow are isotopically 

heavier (less negative) than the stream samples 

collected during intermediate flow. Although the 

samples were not collected during high-flow 

conditions, the relation between the low-flow and the 

intermediate-flow samples suggests that the isotopic 

composition of high-flow waters would be lighter (more 

negative) because of generally cooler temperatures and 

less evaporation during the winter and spring when 

streamflow is highest.

The relatively light (δ18O and δD values less than 

−6.4 and −43 per mil, respectively) isotopic 

composition of samples from sites 6 and 8 on San 

Francisquito Creek (collected during the low-flow 

seepage runs of April 30, 1997, and June 12, 1996, 

respectively) and from the ADO site on Arroyo Ojo de 

Agua (collected on April 30, 1996, a day after the 

intermediate-flow seepage run) may represent mixing 

of natural runoff and imported water. These isotopic 

data and the results of the chemical analysis for sites 6 
Characterization of Surface-Water and Ground-Water Quality 35

Figure 13. Relation between delta deuterium and delta oxygen-18 for (A) all water samples, (B) San Francisquito Creek and Arroyo Ojo de 

Agua Creek samples, and (C) ground-water samples from wells along or near San Francisquito Creek, southern San Mateo and northern 

Santa Clara Counties, California, April 1996 through May 1997.

-110

-100

-90

-80

-70

-60

-50

-40

-30

-20

-10

-14 -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2

Evaporative

 trend line

Deep aquifer—lower zone

Ground water

Surface water

Deep aquifer—upper zone

Shallow aquifer

San Francisquito Creek

 (unless otherwise noted)

Lake Lagunita

Public supply (imported

 Hetch Hetchy water, treated)

A



B



C

DELTA DEUTERIUM, IN PER MIL

DELTA DEUTERIUM, IN PER MIL

DELTA OXYGEN-18, IN PER MIL

DELTA OXYGEN-18, IN PER MIL

Arroyo Ojo de Agua (ADO)

Local meteoric water line

Global meteoric water line (Craig, 1961)

Global meteoric water line 

Ground-water symbol and identifier—number

 in parentheses is chloride concentration in milligrams

 per liter when greater than 100

Local meteoric 

 water line 

Global meteoric

water line 

-70

-60

-50

-40

-30

-9 -8 -7 -6 -5

-60

-50

-40

-30

-20

-8 -7 -6 -5 -4

Intermediate flow—April 29–30, 1996

Intermediate flow—April 29–30, 1996

Low flow—June 12, 1996

Low flow—June 12, 1996

Low flow—April 30, 1997

Low flow—April 30, 1997

Stream-water symbol and identifier

6

6

8 8

8

ADO

9

12

11 LT

6

1 and 3

1 1

3

5

3

36L10

27G1

(160)

1G1

1G1

25F1

27K2 27K2

35D3 25G1

35G10

3M2

11B10

3M10

36F2

36D1

34H1

27R3

2H10

1B2

1B2

Los Trancos Creek (LT)

5

Local meteoric

 water line 

Deep aquifer—

 lower zone

Deep aquifer—

 upper zone

Shallow aquifer 

Group II

Group II

Group I

Group I 3M2

(350)

(230)

(220)

(200)

(180)

(120)
36 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

and 8 (table 7, appendix A) indicate that urban runoff 

from residential irrigation or from other domestic uses 

of imported water constitutes most of the streamflow 

in San Francisquito Creek during low-flow conditions. 

Because Arroyo Ojo de Agua is flanked by residential 

areas upstream of where the isotope sample was collected, urban runoff may account for the isotopic 

composition of this water sample as well.

The δ18O and δD values in ground-water samples 

collected from wells in the study area were isotopically 

lighter than those in the surface-water samples, except 

for the samples from sites 6 and 8 collected during 

low-flow conditions. The δ18O and δD values ranged 

from −5.39 to −8.97 per mil and −38.2 to −66.4 per mil, 

respectively (fig. 13C, table 7). Because evaporative 

effects are minimal once water infiltrates several feet 

below the uppermost layers of soil, any changes in the 

isotopic composition of ground water generally reflect 

mixing of water from different sources of recharge to 

the aquifer system (Fournier and Thompson, 1980; 

Mazor, 1991). Potential sources of recharge include 

infiltration from San Francisquito Creek, leakage from 

public water supply and sewage lines, seepage from 

Lake Lagunita, overwatering of landscaping, underflow 

from adjacent aquifers, infiltration from smaller creeks 

not tributary to San Francisquito Creek, and direct 

recharge of precipitation (Sokol, 1964).

On the basis of the isotopic composition of the 

water samples, most of the isotope samples from the 

wells can be divided into two slightly overlapping 

groups: Group I, which represents all the samples from 

wells in the deep aquifer, and Group II, which 

represents samples from wells in the shallow aquifer 

(fig. 13). Two samples plot in the slightly overlapping 

part of the groups: one sample is from the shallow 

aquifer and one is from the lower zone of the deep 

aquifer. Although ground-water samples were collected 

only once during this study, the isotopic composition of 

the samples reflect the isotopic composition of ground 

water, which for the most part is less affected by 

seasonal or temporal variations in the source water than 

that of surface water (Gat and Gonfiantini, 1981). The 

isotopic composition of samples in Group I can be 

presumed to reflect the long-term average composition 

of local precipitation and other contributing sources of 

recharge. The slightly heavier isotopic composition of 

samples from deep aquifer wells 5S/3W-36D1, 

5S/3W-36F2, 6S/3W-3M10, and 6S/3W-11B10, which 

plot on the right-hand side of Group I (fig. 13C), may 

be a reflection of their proximity to potential sources of 

recharge. Wells 5S/3W-36D1, 5S/3W-36F2, and 

6S/3W-3M10 are located adjacent to or in the vicinity 

of losing reaches of San Francisquito Creek (figs. 8 and 

14). Well 6S/3W-11B10 is the closest well to and 

downgradient of Lake Lagunita (fig. 14), a significant 

source of recharge in the study area according to Sokol 

(1964).

Group II includes four samples from wells 

completed in the shallow aquifer (fig. 13 A and C). The 

δ18O and δD values of one sample plot in the overlap of 

Groups I and II. The isotopic composition of these 

samples trends towards the isotopic composition of 

public supply water. Recharge of imported public 

supply water from leaking supply and (or) sewer lines 

may be a source of the isotopically light water sampled 

from the wells in the shallow aquifer. Return flow of 

imported public supply water used for irrigating 

landscaping may be another contributing source of the 

isotopically light water to shallow wells in the study 

area.

The sample from shallow well 6S/3W-3M2, 

located adjacent to the losing reach of San Francisquito 

Creek between sites 4 and 5 (fig. 14), does not plot in 

either Group I or II (fig. 13). The isotopic composition 

of this sample, collected in early May 1997, plots 

approximate to the isotopic composition of the 

surface-water samples collected from the creek during 

intermediate-flow conditions in late April 1996 even 

though this well was sampled during low-flow 

conditions. Records of daily mean streamflow (fig. 6) 

indicate that intermediate flow-conditions on San 

Francisquito Creek in 1997 occurred between late 

March and mid-April, 3 to 5 weeks prior to sampling 

well 6S/3W-3M2. In comparison, the isotopic 

composition of water from deep aquifer well 

6S/3W-3M10 was significantly heavier (fig. 13), 

despite having the same chemical composition as water 

from 6S/3W-3M2 (fig. 11). The same chemistry but 

different isotopic composition in the water from these 

two wells indicates that there is a time delay as water 

moves from the creek to the shallow aquifer and then to 

the lower aquifer.

The stable isotopes of ground water are useful for 

tracing seawater intrusion because the isotopic 

composition of seawater is constant at about 0 per mil 

(Gat and Gonfiantini, 1981) and most changes in the 

isotope composition of ground water along a flow line 

primarily reflect the mixing of waters within the aquifer 

system. The 18O and δD values of the samples from 

wells with elevated chloride concentrations are the 

same or are lighter than the isotopic values of the 

samples from wells with low chloride concentrations. If 

bay water were the source of the elevated chloride 

concentration in the samples from these wells, these 

samples should be isotopically heavier than the samples 

from the wells with the lower chloride concentrations. 

For example, the sample from well 5S/3W-25F1, 

perforated in the deep aquifer, has the highest chloride 

concentration of all the samples collected from the 

wells in the deep aquifer (350 mg/L); however, this
Characterization of Surface-Water and Ground-Water Quality 37

Figure 14. Delta oxygen-18 and delta deuterium for ground-water samples from wells along or near San Francisquito Creek, southern San 

Mateo and northern Santa Clara Counties, California, April and May 1997.

Woodside 

 

 Rd

El Camino Real

El Camino Real

Middlefield 

Bear Gulch 

Reservoir

Embarcadero Embarcadero 

Alma 

 St



Page Mill Rd

 WEBB RANCH

 (Stanford)

El Camino

Real

Foothill

Exprwy

Arestradero

Rd

Bayshore

Bayshore

Freeway

Freeway

Rd

 PALO ALTO

GOLF COURSE

 MUNICIPAL

Charleston Rd

 Rd

San Antonio

Rd

Searsville

Lake

Junipero

Serra

Freeway

Sand 

Hill

Rd

Mt

Home Rd

Alpine Rd

Junipero Serra

Blvd

Santa Cruz Ave

Alpine Rd

San Francisquito

Creek

Los Trancos Cr

Marsh Rd

Atherton 

 

Ave

Alameda de las 

Woodside Rd

Whiskey Hill Rd

Stanford 

Ave

Jefferson

Ave

Bay

Bay



Rd

Whipple

Ave

El Camino

 Road

Far m

Hill Blv

Cr

Arro yo Ojo de Ag ua

	

 Ave

Matadero

Creek

Deer Cr

Barron 

Real

Atherton

Channel

Rd

Rd

Cordilleras

37°

30'

T 5 S

T 6 S

37°

27'

30"

37°

25'

0

0

1

1

2

2

3 Miles

3 Kilometers

Ravenswood Point

Creek

Pulgas

Adobe Creek





 Lake 

Lagunita

 STANFORD 

GOLF COURSE

Sand Hill 

 Rd

Contact between partly consolidated and consolidated bedrock assemblages (hachured side)

 and unconsolidated alluvium

Redwood

Cre ek

HETCH HETCHY

HETCH HETCHY

AQUEDUCT

AQUEDUCT

















 

 





1

2

LT

4

5

7

10

6

11

12

LL

ADO

Sand Point

84

82

Rd

Dumbarton Bridge

Willow











	




City Hall

City Hall

City Hall

Stanford University

SALT EVAPORATORS SALT EVAPORATORS

SALT EVAPORATORS

SALT EVAPORATORS

 SALT 

EVAPORATORS

Redwood City

Atherton

Menlo Park Palo Alto

 East

 Palo Alto

San Francisco Bay

Bayfront Expwy

Ave

Hamilton

Chilco St

-59.6

-46.7 -48.4

-45.8

-43.5

-38.2

-38.2

-42.9

-42.9

-40.8

-40.8

-53.6

-66.4

-45.3

-49.6

-43.8

-41.6

122°15' R 4 W R 3 W 122°12'30" 122°10' R 3 W 122°07'30" R 2 W

Base from U.S. Geological Survey

1:24,000 Palo Alto, 1991

-8.14

-6.78 -7.12

-6.44

-5.39

-6.01

-6.16

-6.52

-6.16

-6.1

-6.32

-6.02

-7.48

-5.81

-6.01

-7.23

-6.58

11B10

3M2

3M10

1G1

1B2

36L10

36F1

2H10

34H1

27K2 27R3

35D3 36D1

35G10

25F1

25G1 27G1

 Wells and number—Upper number is delta oxygen-18 and lower number is delta deuterium, in per mil, in italics 

EXPLANATION

 3

Shallow aquifer

Deep aquifer–upper zone

Deep aquifer–lower zone

9

8

11164500

San

Francisquito

Creek

-8.97

-6.65 -41.8

-41.8

-43.2

Pulgas Fault

-5.39

280

101

3M2

3M10

36D1

Woodland Ave

E. Bayshore Rd E. Bayshore Rd

San Mateo Dr

Pier St



3

4

11164500

Temporary streamflow-measurement station and station identifier

Stream-gaging station and identifier (11164500) and temporary site identifier (3)—Site 3 

 is a temporary streamflow measurement station adjacent to permanent stream-gaging station 
38 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

sample has the lightest isotopic composition of any 

well sampled in the deep aquifer (appendix A and table 

7, respectively. The isotopic and trace-element data 

presented earlier indicate that bay water intrusion is 

not the source of the high chloride concentrations in 

samples from wells collected for this study.

SUMMARY AND CONCLUSIONS 

San Francisquito Creek, located in southern San 

Mateo and northern Santa Clara Counties, is an 

important source of ground-water recharge to the 

aquifers of the San Francisquito Creek alluvial fan 

which, in turn, is a significant source of water to some 

communities in the study area. Local residents are 

concerned that infiltration, and consequently 

ground-water recharge, may be reduced if additional 

flood-control measures are implemented along San 

Francisquito Creek.

Streamflow measurements made in 1996 and 

1997 at 13 temporary streamflow-measurement stations 

were used to estimate gains and losses along selected 

reaches of San Francisquito Creek. Streamflow 

measurements made during five seepage runs between 

April 1996 and May 1997 and historical streamflow 

records for USGS stream gage 11164500 for water 

years 1932–41 and 1951–99 were used to estimate 

recharge from San Francisquito Creek to the underlying 

aquifers of the San Francisquito Creek alluvial fan. 

Water samples were collected from 17 wells, 

9 streamflow-measurement sites, and 3 miscellaneous 

surface-water sites for analysis of major ions, trace 

elements, silica, nutrients, and stable isotopes of 

oxygen (oxygen-18) and hydrogen (deuterium). 

Chemistry data were used to help characterize the 

quality of surface and ground water and to help assess 

the source of ground water to wells.

San Francisquito Creek and its tributaries drain a 

basin of approximately 45 square miles, including 

37.4 square miles of hilly to mountainous terrain on the 

eastern slope of the Santa Cruz Mountains and 

approximately 7.5 square miles of gently sloping 

alluvial plain that includes parts of Menlo Park, Palo 

Alto, East Palo Alto, and Stanford University. Except 

where flood-control measures have been implemented 

along some lower reaches of San Francisquito Creek, 

the creek remains in a near-natural state along about 

half of its 12.7-mile length. Streamflow is almost 

entirely dependent on annual rainfall, which occurs 

primarily during November through April. As a 

consequence of this seasonal rainfall pattern and a 

water table that is below the channel bottom along most 

of San Francisquito Creek, natural flows downstream 

from the Pulgas Fault and streamflow-measurement 

site 4 usually are nonexistent for about 6 months of the 

year.

The San Francisquito Creek alluvial fan forms an 

arbitrarily defined ground-water subbasin of the Santa 

Clara Valley, which encompasses an area of 

approximately 22 square miles in southern San Mateo 

and northern Santa Clara Counties. The San 

Francisquito Creek alluvial fan consists of two 

identifiable aquifers: a shallow aquifer extending from 

near land surface to depths of about 15 to 100 feet 

below land surface, and a deep aquifer consisting of two 

water-bearing zones—an upper zone extending to 

depths between about 200 to 300 feet below land 

surface and a lower zone extending to depths greater 

than 300 feet. The shallow and deep aquifers are 

separated by a laterally extensive clay bed that may be 

continuous across much of the alluvial fan. In areas 

distant from the bay where this clay bed is 

discontinuous or absent, such as in areas upslope of the 

approximate midway point between San Mateo Drive 

and Alma Street (sites 5 and 6, respectively) on San 

Francisquito Creek, recharge from the shallow aquifer 

may have a direct hydrologic connection to the 

deep-aquifer zones.

Streamflow measurements made on San 

Francisquito and Los Trancos Creeks three times during 

low-flow conditions, once during intermediate-flow 

conditions, and once during high-flow conditions 

indicate that San Francisquito Creek generally is a 

losing stream. Streamflow measurements for the 

upstream reaches of San Francisquito Creek between 

Webb Ranch (site 1) and Sand Hill Road (site 4) 

showed relatively small changes compared with the 

streamflow measurements for the reaches downstream 

from site 4. Streamflow losses between site 1 and Pier 

Street (site 2) averaged 0.8 acre-feet per day (acre-ft/d). 

Streamflow losses between sites 2 and 4 were negligible 

for each of the two reaches, averaging only 0.1 acre-feet 

per day.

Streamflow measurements indicate that 

streamflow losses increase downstream from the Pulgas 

Fault at site 4. Streamflow losses between this site and 

San Mateo Drive (site 5) averaged 1.1 acre-ft/d. The 

greatest streamflow losses were measured along a 

1.8-mile section of the creek between the San Mateo 

Drive bike bridge (site 5) and Middlefield Road (site 7). 

Losses between San Mateo Drive (site 5) and Alma 

Street (site 6) averaged 3.1 acre-ft/d for three seepage 

runs (April 29, 1996; February 25–27, 1997; and 

April 30, 1997) and losses between Alma Street and 

Middlefield Road (sites 6 and 7, respectively) averaged 

2.5 acre-ft/d for two seepage runs (April 29, 1996, and 

February 25–27, 1997).

Downstream from Middlefield Road (site 7), 

streamflow gains and losses owing to seepage may be 
Summary and Conclusions 39

masked by urban runoff, changes in bank storage, and 

tidal effects from San Francisco Bay. Streamflow gains 

measured between Middlefield Road and the 

1200 block of Woodland Avenue (site 8) averaged 

0.8 acre-ft/d. The streamflow gains measured in this 

reach may be attributable to either urban runoff and (or) 

ground-water inflow. Below the 1200 block of 

Woodland Avenue, San Francisquito Creek again 

becomes a losing stream; losses averaged 1.6 acre-ft/d 

between the 1200 block of Woodland Avenue and 

University Avenue (site 9) and 1.0 acre-ft/d between 

University Avenue and Newell Road (site 10). 

Discharge from a large storm drain between Newell 

Road (site 10) and East Bayshore Road (site 11) may 

account for streamflow gains of 1.0 and 0.8 acre-ft/d 

measured during the April 1996 and February 1997 

seepage runs, respectively. The reach between East 

Bayshore Road and the Palo Alto Municipal Golf 

Course (site 12) is difficult to characterize because of 

the probable influence of high tides as far upstream as 

East Bayshore Road. A loss of 0.8 acre-ft/d was 

measured during the April 1996 seepage run and a gain 

of 1.6 acre-ft/d was measured during the February 1997 

seepage run.

Estimated average streamflow losses totaled 

approximately 1,050 acre-feet per year for the reaches 

between USGS stream gage 11164500 at Stanford 

(site 3) and the Palo Alto Municipal Golf Course 

(site 12), including approximately 595 acre-feet per 

year for the 1.8-mile section between San Mateo Drive 

(site 5) and Middlefield Road (site 7). After accounting 

for evapotranspiration, recharge to ground water from 

San Francisquito Creek may total as much as 950 acrefeet during an average year; about 58 percent, or 

550 acre-feet, of this total occurs between San Mateo 

Drive (site 5) and Middlefield Road (site 7).

Measurements of specific conductance indicate 

that the dissolved-solids concentrations of San 

Francisquito Creek water may vary as a function of 

seasonal changes in hydrologic conditions. During 

periods of dry weather and low flow, the dissolvedsolids concentrations in stream water tends to be high, 

and during periods of wet weather, the concentration 

tends to be low owing to dilution by surface water. 

Several samples collected during the low-flow seepage 

runs at Alma Street (site 6) and the 1200 block of 

Woodland Avenue (site 8) had lower specific 

conductance values than the upstream samples. 

Concentrations of magnesium, sodium, chloride, 

boron, and total dissolved solids also were lower in the 

samples from Alma Street (site 6) and the 1200 block of 

Woodland Avenue (site 8) than in the samples from the 

upstream sites. Nutrient concentrations generally were 

higher in downstream sites than upstream sites. These 

differences in specific conductance and in the chemical 

composition of water from the upstream and 

downstream sites indicate that during low-flow 

conditions water downstream from San Mateo Drive 

(site 5) is a mixture of natural streamflow and urban 

runoff.

The chemical composition of ground water in the 

study area varies widely and primarily as a function of 

aquifer depth. The composition of ground water 

changes from a calcium-bicarbonate or mixed cationbicarbonate water in the shallow aquifer to a sodiumchloride or mixed cation-mixed anion water in the 

lower zone of the deep aquifer. Most of the samples plot 

within three distinct groups on the central diamond of a 

trilinear diagram: (1) samples (predominantly from the 

shallow aquifer) with a composition similar to the 

composition of surface-water samples from San 

Francisquito Creek and Lake Lagunita, (2) samples 

(predominantly from the shallow aquifer) with higher 

percentages of bicarbonate and lower percentages of 

sulfate than those for the samples from group 1, and (3) 

samples (from the deep aquifer) characterized by higher 

percentages of chloride and sodium and lower 

percentages of calcium, magnesium, and bicarbonate 

than those in the samples from groups 1 and 2.

The relation between water chemistry and 

aquifer depth may be attributed to natural systematic 

changes in the composition of ground water as it 

circulates through different geologic materials. The 

most pronouced difference in the composition of 

ground water between the shallow aquifer and the deep 

aquifer occurs where the two aquifers are separated by 

extensive deposits of bay mud and clay. Ground water 

that encounters these deposits can become modified by 

cation exchange. Upstream of Alma Street (site 6), 

where the clay deposits are minimal or nonexistent, the 

differences in ground-water composition between the 

shallow and deep aquifer are much less pronounced.

Analysis of trace-element data shows that water 

from the shallow and deep aquifers of the San 

Francisquito Creek alluvial fan generally have ratios of 

chloride-to-boron, bromide, and iodide, with respect to 

chloride concentration, dissimilar to ratios for water 

from San Francisco Bay and seawater. These ratios, 

particularly the chloride-to-iodide ratios, indicate that 

modern bay water intrusion is not the source of the 

higher chloride water in some of the wells. Dissolution 

of chloride-rich marine sediments located within and 

underlying the aquifer system probably is the source of 

the water containing high chloride concentrations 

(greater than 100 milligrams per liter) in the samples 

collected as part of this study.

The δ18O and δD composition of almost all 

waters sampled for this study plot below, but parallel to, 

the global meteoric water line along a line known as the 

local meteoric water line. The isotopically heaviest 
40 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

(least negative) water was from Lake Lagunita and 

plots to the right of the local meteoric water line 

because it is partly evaporated. The isotopically lightest 

(most negative) water was associated with public 

supply water imported to the study area from the Hetch 

Hetchy Reservoir in the Sierra Nevada. Except for the 

low-flow samples from Alma Street (site 6) and the 

1200 block of Woodland Avenue (site 8), the stream 

samples were isotopically heavier than the groundwater samples. The fairly light isotopic composition of 

the samples from Alma Street (site 6) and the 1200 

block of Woodland Avenue (site 8) on San Francisquito 

Creek and the water-chemistry data for these sites 

indicate that urban runoff from residential irrigation or 

from other domestic uses of imported water constitutes 

most of the streamflow during low-flow conditions.

The isotopic composition of most of the 

ground-water samples plot within two slightly 

overlapping groups on a plot of δ18O and δD. Group I 

represents all the samples from wells in the deep 

aquifer and several samples from wells in the shallow 

aquifer. The slightly heavier isotopic composition of 

four deep aquifer samples that plot on the right-hand 

side of this group may be a reflection of their proximity 

to potential sources of recharge. Three of these wells 

are located in the vicinity of losing reaches of San 

Francisquito Creek and the fourth is the closest well to 

and downgradient of Lake Lagunita, which reportedly 

is a significant source of recharge in the study area. 

Group II includes samples from wells completed in the 

shallow aquifer. The isotopic composition of these 

samples trends towards the isotopic composition of 

public supply water. Recharge of imported public 

supply water from leaking supply and (or) sewer lines 

may be the source of the isotopically light water 

sampled from these wells. Additional isotope samples 

need to be collected, particularly from San Francisquito 

Creek during high-flow streamflow conditions, to 

determine if the isotopic composition of the 

ground-water samples is within the expected range of 

natural recharge.

Analyses of the isotopic results of the 

ground-water samples collected as part of this study 

provide further evidence that the intrusion of bay water 

is not the source of water to the wells with high chloride 

concentrations sampled as part of this study. The 

isotopic composition of all the samples from the wells 

with high chloride concentrations was the same or 

lighter than the isotopic composition of the samples 

from the wells that have low chloride concentrations. If 

bay water was the source of the water with high 

chloride concentrations the iosotopic composition of 

the samples affected by bay water intrusion should be 

significantly heavier than samples of native ground 

water.

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evapotranspiration investigations in the San Francisco 

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sediments: U.S. Geological Survey Open-File Report 

93-125, 217 p.

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545 p.
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Fournier, R.D., and Thompson, J.M., 1980, The recharge 

area for the Coso, California, Geothermal system 

deduced from δD and δ18O in thermal and nonthermal 

waters in the region: U.S. Geological Survey Open-File 

Report 80-454, 27 p.

Freeze, R.A., and Cherry, J.A., 1979, Groundwater: 

Englewood Cliffs, New Jersey, Prentice-Hall, 604 p.

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hydrology, deuterium and oxygen-18 in the water cycle: 

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characteristics of natural water: U.S. Geological Survey 

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saltwater infiltration, and ground-surface recession in 

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Transactions of 1940 of the American Geophysical 

Union, pt. 1, p. 23–35.

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Francisquito Creek, San Mateo and Santa Clara 

Counties, California, for flood control and allied 

purposes: San Francisco, Calif., U.S. Army Engineer 

District, 27 p., 7 plates.

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42 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Appendix A. Field measurements and laboratory analyses of samples from ground-water wells, streamflow-measurement stations, Lake 

Lagunita, and public supply, southern San Mateo and northern Santa Clara Counties, California, 1996–97

[See figure 10 for location of wells and figure 2 for location of streamflow-measurement stations. USGS (U.S. Geological Survey) identification No. consists 

of latitude, longitude, and sequence number. Parameter code, in brackets, is a 5-digit number in the U.S. Geological Survey computerized data system, 

National Water Infomration System (NWIS), used to uniquely identify a specific constituent or property. Flow-condition rating (based on instantaneous 

streamflow at USGS stream gage 11164500): H, high flow; I, intermediate flow; L, low flow. CaCO3, calcium carbonate; ft3

/s, cubic foot per second; μS/cm, 

microsiemen per centimeter at 25°C; °C, degree Celsius; mg/L, milligram per liter; μg/L, microgram per liter. <, actual value is less than value shown; —, no 

data] 

See footnotes at end of table.

State well No. 

or 

site identifier 

(source of 

sample)

USGS 

identification No.

Sample

date

Instantaneous

streamflow

(ft3/s)

Flowcondition 

rating

Field measurements

pH

(standard

units)

Specific conductance 

(μS/cm)

Temperature,

water

(°C)

Alkalinity

(mg/L as

CaCO3)

Bicarbonate

(mg/L)

[00061] [00400] [00095] [00010] [39086] [00453]

Streamflow-measurement stations

Site 1 372426122120301 4-29-96

6-12-96

7-22-96

2-25-97

6.46

1.66

.27

14.7

I 

L

L

H

—

—

—

—

—

870

1,140

742

17.0

16.5

—

10.5

—

—

—

—

—

—

—

—

Site 2 372450122113001 4-29-96

6-12-96

2-25-97

6.22

1.86

13.5

I

L

H

—

—

—

—

930

764

17.0

16.5

11.0

—

—

—

—

—

—

Site LT 372447122112701 7-22-96

2-25-97

.44

4.91

L

H

—

—

1,220

730

—

12.0

—

—

—

—

Site 3 372524122111801 4-29-96

6-12-96

7-22-96

2-25-97

4-30-97

6.62

1.18

1.04

19.0

1.97

I

L

L

H

L

—

—

—

—

8.3

—

980

1,270

765

945

15.0

17.0

—

10.0

17.0

—

—

—

—

250

—

—

—

—

300

Site 4 372547122112001 4-29-96

6-12-96

2-26-97

6.20

1.33

19.3

I

L

H

—

—

—

—

1,060

772

16.0

18.0

10.5

—

—

—

—

—

—

Site 5 372622122104401 4-29-96

6-12-96

7-22-96

2-26-97

4-30-97

5.96

.26

.09

19.1

1.36

I

L

L

H

L

—

—

—

—

8.0

—

1,030

1,270

780

985

17.5

21.5

—

10.5

20.0

—

—

—

—

240

—

—

—

—

300

Site 6 372651122100401

1 372651122100901

4-29-96

2-26-97

4-30-97

3.83

17.8

.07

I

H

L

—

—

8.3

—

770

580

20.0

12.0

21.5

—

—

150

—

—

180

Site 7 372713122094201 4-29-96

2-26-97

2.49

16.6

I

H

—

—

—

772

21.5

12.5

—

—

—

—

Site 8 372727122090001 6-12-96

2-26-97

4-30-97

.28

17.6

.19

L

H

L

—

—

8.2

770

770

754

22.0

13.0

19.5

—

—

230

—

—

280

Site 9 372726122082401 4-29-96

2-26-97

1.90

16.6

I

H

—

—

—

770

22.5

13.0

—

—

—

—

Site 10 372716122080801 4-29-96

2-27-97

2.14

15.4

I

H

—

—

—

772

22.5

11.0

—

—

—

—

Site 11 372713122073401 4-29-96

2-27-97

2.64

15.9

I

H

—

—

—

785

23.0

11.5

—

—

—

—

Site 12 372719122071501 4-29-96

2-27-97

2.20

16.6

I

H

—

—

—

801

27.0

12.5

—

—

—

—

Lake Lagunita and public supply

Lake Lagunita 372523122102401 4-30-97 — 8.4 660 18.5 180 220

Public supply 2 4-28-97 — 7.9 77 16.5 26 32
Appendix A 43

Appendix A. Field measurements and laboratory analyses of samples from ground-water wells, streamflow-measurement stations, Lake 

Lagunita, and public supply, southern San Mateo and northern Santa Clara Counties, California, 1996–97 —Continued

See footnotes at end of table.

State well No. 

or

site identifier 

(source of

sample)

Sample

date

Hardness, 

total

(mg/L as

CaCO3)

Calcium, 

dissolved

(mg/L)

Magnesium, dissolved

(mg/L)

Potassium, 

dissolved

(mg/L)

Sodium adsorption

ratio

Sodium, 

dissolved

(mg/L)

Sodium 

percent

[00900] [00915] [00925] [00935] [00931] [00930] [00932]

Streamflow-measurement stations—Continued

Site 1 4-29-96

6-12-96

7-22-96

2-25-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 2 4-29-96

6-12-96

2-25-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site LT 7-22-96

2-25-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 3 4-29-96

6-12-96

7-22-96

2-25-97

4-30-97

—

—

—

—

370

—

—

—

—

85

—

—

—

—

39

—

—

—

—

2

—

—

—

—

1

—

—

—

—

53

—

—

—

—

24

Site 4 4-29-96

6-12-96

2-26-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 5 4-29-96

6-12-96

7-22-96

2-26-97

4-30-97

—

—

—

—

380

—

—

—

—

84

—

—

—

—

42

—

—

—

—

2

—

—

—

—

1

—

—

—

—

55

—

—

—

—

24

Site 6 4-29-96

2-26-97

4-30-97

—

—

210

—

—

49

—

—

21

—

—

2

—

—

1

—

—

32

—

—

25

Site 7 4-29-96

2-26-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 8 6-12-96

2-26-97

4-30-97

—

—

300

—

—

78

—

—

25

—

—

2

—

—

.9

—

—

36

—

—

21

Site 9 4-29-96

2-26-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 10 4-29-96

2-27-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 11 4-29-96

2-27-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 12 4-29-96

2-27-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Lake Lagunita and public supply—Continued

Lake Lagunita 4-30-97 240 53 26 2 1 35 25

Public supply 2 4-28-97 21 6.4 1.2 .5 .5 5 34
44 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Appendix A. Field measurements and laboratory analyses of samples from ground-water wells, streamflow-measurement stations, Lake 

Lagunita, and public supply, southern San Mateo and northern Santa Clara Counties, California, 1996–97 —Continued

See footnotes at end of table.

State well No. 

or 

site identifier 

(source of 

sample)

Sample

date

Chloride,

dissolved

(mg/L)

Fluoride,

dissolved

(mg/L)

Silica,

dissolved

(mg/L)

Sulfate,

dissolved

(mg/L)

Nitrogen,

ammonia,

dissolved

(mg/L)

Nitrite plus 

nitrate as N, 

dissolved

(mg/L)

Nitrogen,

nitrite, 

dissolved 

(mg/L)

[00940] [00950] [00955] [00945] [00608] [00631] [00613]

Streamflow-measurement stations—Continued

Site 1 4-29-96

6-12-96

7-22-96

2-25-96

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—.

Site 2 4-29-96

6-12-96

2-25-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site LT 7-22-96

2-25-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 3 4-29-96

6-12-96

7-22-96

2-25-97

4-30-97

—

—

—

—

62

—

—

—

—

0.3

—

—

—

—

16

—

—

—

—

150

—

—

—

—

<0.02

—

—

—

—

1.4

—

—

—

—

<0.01

Site 4 4-29-96

6-12-96

2-26-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 5 4-29-96

6-12-96

7-22-96

2-26-97

4-30-97

—

—

—

—

70

—

—

—

—

.3

—

—

—

—

15

—

—

—

—

170

—

—

—

—

<.02

—

—

—

—

1.4

—

—

—

—

<.01

Site 6 4-29-96

2-26-97

4-30-97

—

—

39

—

—

.4

—

—

12

—

—

80

—

—

<.02

—

—

.32

—

—

<.01

Site 7 4-29-96

2-26-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 8 6-12-96

2-26-97

4-30-97

—

—

47

—

—

.2

—

—

18

—

—

94

—

—

<.02

—

—

2.2

—

—

.01

Site 9 4-29-96

2-26-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 10 4-29-96

2-27-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 11 4-29-96

2-27-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 12 4-29-96

2-27-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Lake Lagunita and public supply—Continued

Lake Lagunita 4-30-97 44 0.2 12 90 <0.02 <0.05 <0.01

Public supply 2 4-28-97 3.7 1.0 6 5.7 <.02 .07 <.01
Appendix A 45

Appendix A. Field measurements and laboratory analyses of samples from ground-water wells, streamflow-measurement stations, Lake 

Lagunita, and public supply, southern San Mateo and northern Santa Clara Counties, California, 1996–97 —Continued

See footnotes at end of table.

State well No. 

or

site identifier 

(source of 

sample)

Sample 

date

Phosphorus,

ortho,

dissolved

(mg/L)

Dissolved

solids, 

total 

(mg/L)

Boron, 

dissolved

(μg/L)

Bromide, 

dissolved

(mg/L)

Iodide, 

dissolved

(mg/L)

Iron,

dissolved

(μg/L)

Manganese, 

dissolved

(μg/L)

[00671] [70301] [01020] [71870] [71865] [01046] [01056]

Streamflow-measurement stations—Continued

Site 1 4-29-96

6-12-96

7-22-96

2-25-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 2 4-29-96

6-12-96

2-25-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site LT 7-22-96

2-25-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 3 4-29-96

6-12-96

7-22-96

2-25-97

4-30-97

—

—

—

—

0.04

—

—

—

—

563

—

—

—

—

320

—

—

—

—

0.13

—

—

—

—

0.027

—

—

—

—

<3

—

—

—

—

11

Site 4 4-29-96

6-12-96

2-26-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 5 4-29-96

6-12-96

7-22-96

2-26-97

4-30-97

—

—

—

—

.03

—

—

—

—

591

—

—

—

—

300

—

—

—

—

.14

—

—

—

—

.026

—

—

—

—

<3

—

—

—

—

2

Site 6 4-29-96

2-26-97

4-30-97

—

—

.06

—

—

327

—

—

160

—

—

.078

—

—

.015

—

—

10

—

—

7

Site 7 4-29-96

2-26-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 8 6-12-96

2-26-97

4-30-97

—

—

.04

—

—

447

—

—

190

—

—

.15

—

—

.005

—

—

<3

—

—

3

Site 9 4-29-96

2-26-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 10 4-29-96

2-27-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 11 4-29-96

2-27-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Site 12 4-29-96

2-27-97

—

—

—

—

—

—

—

—

—

—

—

—

—

—

Lake Lagunita and public supply—Continued

Lake Lagunita 4-30-97 0.03 371 190 0.035 0.015 <3 3

Public supply 2 4-28-97 <.01 46 30 <.01 .002 18 1
46 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Appendix A. Field measurements and laboratory analyses of samples from ground-water wells, streamflow-measurement stations, Lake 

Lagunita, and public supply, southern San Mateo and northern Santa Clara Counties, California, 1996–97 —Continued

State well No. 

or

site identifier 

(source of 

sample)

USGS

identification No.

Sample

date

Field measurements

pH

(standard

units)

Specific

conductance, 

(μS/cm)

Temperature,

water

(°C)

Alkalinity,

(mg/L as

CaCO3)

Bicarbonate

(mg/L)

[00400] [00095] [00010] [39086] [00453]

Well sites

5S/3W-25F1 372818122082801 5-02-97 7.9 1,550 21.0 190 230

5S/3W-25G1 372809122081501 5-01-97 6.5 1,540 17.5 370 450

5S/3W-27G1 372809122102101 4-29-97 6.5 1,740 17.5 500 610

5S/3W-27K2 372756122102501 4-29-97 7.3 1,170 21.5 190 230

5S/3W-27R3 372747122100701 4-29-97 7.2 886 18.5 320 390

5S/3W-34H1 372722122100501 5-01-97 7.5 785 19.5 210 260

5S/3W-35D3 372738122100401 4-29-97 7.2 845 20.0 220 270

5S/3W-35G10 372720122091501 5-01-97 7.1 1,130 20.0 210 260

5S/3W-36D1 372733122085701 5-02-97 7.1 744 18.5 220 260

5S/3W-36F2 372727122084001 4-28-97 7.0 678 18.0 200 240

5S/3W-36L10 372703122083201 4-28-97 6.6 1,050 17.5 370 450

6S/3W-1B2 372640122082401 5-01-97 7.2 1,030 23.5 200 240

6S/3W-1G1 372625122081301 4-28-97 6.5 1,000 17.0 330 400

6S/3W-2H10 372631122091001 4-28-97 7.7 808 19.5 290 350

6S/3W-3M2 372620122105601 5-01-97 6.5 858 14.5 250 300

6S/3W-3M10 372616122105301 5-02-97 6.7 924 16.0 260 320

6S/3W-11B10 372545122092001 5-02-97 7.6 934 21.5 200 240
Appendix A 47

Appendix A. Field measurements and laboratory analyses of samples from ground-water wells, streamflow-measurement stations, Lake 

Lagunita, and public supply, southern San Mateo and northern Santa Clara Counties, California, 1996–97 —Continued

State well No. 

or

site identifier 

(source of

sample)

Sample

date

Hardness,

total

(mg/L as

CaCO3)

Calcium, 

dissolved

(mg/L)

Magnesium,

dissolved

(mg/L)

Potassium, 

dissolved

(mg/L)

Sodium adsorption ratio

Sodium, 

dissolved

(mg/L)

Sodium 

percent

[00900] [00915] [00925] [00935] [00931] [00930] [00932]

Well sites—Continued

5S/3W-25F1 5-02-97 220 51 23 1 6 210 68

5S/3W-25G1 5-01-97 560 160 37 2 2 88 26

5S/3W-27G1 4-29-97 640 160 58 .5 2 100 26

5S/3W-27K2 4-29-97 230 60 18 2 4 130 55

5S/3W-27R3 4-29-97 300 86 21 1 .9 36 21

5S/3W-34H1 5-01-97 160 44 12 1 3 92 55

5S/3W-35D3 4-29-97 200 54 15 2 3 90 50

5S/3W-35G10 5-01-97 210 57 16 1 4 140 60

5S/3W-36D1 5-02-97 190 54 14 2 2 74 46

5S/3W-36F2 4-28-97 220 63 15 2 1 50 33

5S/3W-36L10 4-28-97 370 100 27 .6 1 58 26

6S/3W-1B2 5-01-97 130 35 9.6 1 6 160 73

6S/3W-1G1 4-28-97 350 95 28 .9 2 66 29

6S/3W-2H10 4-28-97 280 86 17 2 1 39 23

6S/3W-3M2 5-01-97 330 87 28 2 1 46 24

6S/3W-3M10 5-02-97 360 97 28 2 1 45 22

6S/3W-11B10 5-02-97 210 60 15 1 3 99 51
48 Streamflow Gains and Losses along San Francisquito Creek and Characterization of Surface- and Ground-Water Quality, California, 1996–97

Appendix A. Field measurements and laboratory analyses of samples from ground-water wells, streamflow-measurement stations, Lake 

Lagunita, and public supply, southern San Mateo and northern Santa Clara Counties, California, 1996– 97 —Continued

State well No. 

or 

site identifier 

(source of 

sample)

Sample 

date

Chloride, 

dissolved 

(mg/L)

Fluoride, 

dissolved

(mg/L)

Silica,

dissolved 

(mg/L)

Sulfate,

dissolved 

(mg/L)

Nitrogen, 

ammonia, 

dissolved 

(mg/L)

Nitrite plus 

nitrate as N, 

dissolved

(mg/L)

Nitrogen, nitrite, 

dissolved

(mg/L)

[00940] [00950] [00955] [00945] [00608] [00631] [00613]

Well sites—Continued

5S/3W-25F1 5-02-97 350 0.1 25 29 0.32 <0.05 <0.01

5S/3W-25G1 5-01-97 220 .2 29 100 <.02 3.3 .03

5S/3W-27G1 4-29-97 160 .3 32 140 <.02 4.4 <.01

5S/3W-27K2 4-29-97 230 .2 29 37 .15 <.05 <.01

5S/3W-27R3 4-29-97 53 .2 28 68 .06 1.6 .02

5S/3W-34H1 5-01-97 93 .2 25 43 <.02 .90 <.01

5S/3W-35D3 4-29-97 95 .2 26 44 .04 1.7 <.01

5S/3W-35G10 5-01-97 200 .2 26 41 .15 .67 <.01

5S/3W-36D1 5-02-97 61 .2 25 57 <.02 .93 <.01

5S/3W-36F2 4-28-97 39 <.1 29 55 <.02 .32 <.01

5S/3W-36L10 4-28-97 54 .2 30 70 <.02 5.8 <.01

6S/3W-1B2 5-01-97 180 .1 31 44 .12 <.05 <.01

6S/3W-1G1 4-28-97 54 .2 30 71 <.02 2.7 .01

6S/3W-2H10 4-28-97 44 .2 31 69 .22 <.05 <.01

6S/3W-3M2 5-01-97 58 .1 21 140 <.02 1.7 <.01

6S/3W-3M10 5-02-97 72 .2 23 130 <.02 2.7 <.01

6S/3W-11B10 5-02-97 120 .1 29 50 <.02 1.6 <.01
Appendix A 49

Appendix A. Field measurements and laboratory analyses of samples from ground-water wells, streamflow-measurement stations, Lake 

Lagunita, and public supply, southern San Mateo and northern Santa Clara Counties, California, 1996–97 —Continued

1

 Sample collected approximately 400 feet upstream of site 6 on indicated date.

2 Imported water from Hetch Hetchy aqueduct collected from a residential tap in Palo Alto.

State well No.

or 

site identifier 

(source of 

sample)

Sample 

date

Phosphorus,

ortho,

dissolved 

(mg/L)

Dissolved 

solids, 

total 

(mg/L)

Boron,

dissolved 

(μg/L)

Bromide, 

dissolved 

(mg/L)

Iodide,

dissolved 

(mg/L)

Iron,

dissolved 

(μg/L)

Manganese, 

dissolved 

(μg/L)

[00671] [70301] [01020] [71870] [71865] [01046] [01056]

Well sites—Continued

5S/3W-25F1 5-02-97 0.12 802 230 0.98 0.601 47 160

5S/3W-25G1 5-01-97 .06 882 350 .87 .047 <3 35

5S/3W-27G1 4-29-97 .08 976 520 .44 .003 <3 2

5S/3W-27K2 4-29-97 .05 613 660 .67 .552 18 82

5S/3W-27R3 4-29-97 .14 492 200 .22 .015 9 500

5S/3W-34H1 5-01-97 .03 442 170 .28 .259 <3 56

5S/3W-35D3 4-29-97 .05 469 190 .28 .289 <3 46

5S/3W-35G10 5-01-97 .05 615 300 .74 .416 42 110

5S/3W-36D1 5-02-97 .06 422 180 .2 .138 <3 38

5S/3W-36F2 4-28-97 .04 373 200 .11 .078 <3 44

5S/3W-36L10 4-28-97 .05 588 270 .29 .003 <3 <1

6S/3W-1B2 5-01-97 .06 581 390 .61 .365 59 120

6S/3W-1G1 4-28-97 .06 555 260 .36 .008 8 19

6S/3W-2H10 4-28-97 .21 462 180 .22 .009 77 200

6S/3W-3M2 5-01-97 .04 536 210 .19 .005 <3 <1

6S/3W-3M10 5-02-97 .03 563 200 .25 .003 <3 <1

6S/3W-11B10 5-02-97 .08 502 170 .42 .108 6 120