*USGS
science for a changing world
Introduction to NAWOA
In 1991, the National Water-Quality
Assessment (NAWQA) Program of the
U.S. Geological Survey began to address
the need for consistent and scientifically
sound information for managing the
Nation’s water resources. The long-
term goals of this program are to assess
the status of the quality of freshwater
streams and aquifers, to describe trends
or changes in water quality over time,
and to provide a sound understanding
of the natural and human factors that
affect the quality of these resources
(Hirsch and others, 1988). Investigations
are being conducted within major river
basins and aquifer systems, or “study
units,” throughout the Nation to provide
a framework for national and regional
water-quality assessments.
In 2001, the NAWQA Program began
its second decade of intensive water-qual-
ity assessments. Forty-two of the original
59 study units (reduced by elimination
or combination) are being revisited
(Gilliom and others, 2001). The San
Joaquin–Tulare Basins study unit (fig. 1),
located in central California, was a part
of the first decadal cycle of the Program
investigations and remains in the second
cycle.
The three goals upon which the
Program was based remain the founda-
tion of the national assessment in the
Second cycle. During the second cycle,
less emphasis, however, will be placed on
Water-Ouality Assessment of the San Joaquin–Tulare Basins
Entering a New Decade
assessing the status of water-quality con-
ditions because of Substantial advances
made in the assessments during the first
cycle. The focus of the new status assess-
ments will be on sampling water quality
in geographic regions not sampled during
the first cycle and on analyzing selected
constituents not analyzed during the first
cycle.
More emphasis will be placed on
describing long-term trends and on
understanding human and natural factors
that control water quality. Long-term
trends will be studied by resampling
stream and well sites established in the
first cycle. Understanding factors that
control water quality will be addressed in
five topical studies that will study the link
between sources and transport processes,
and potential effects of contaminants on
humans and aquatic ecosystems. This
information will provide a scientific
basis for water-quality management and
the possibility of extrapolating to other
unmonitored areas. The five topical stud-
ies are:
1. Effects of nutrient enrichment on
Stream ecosystems.
2. Agricultural chemicals: Sources,
transport, and fate.
3. Transport of anthropogenic and
natural contaminants to community
Supply wells.
4. Effects of urbanization on Stream
ecosystems.
5. Mercury bioaccumulation in stream
ecosystems.
\ ground water?
( National Water-Quality Assessment Goals
* What is the condition of our Nation’s streams and ground water?
* How is water quality changing over time?
* How do natural features and human activities affect the quality of streams and
Q º
The goals of NAWQA are to assess the status and trends of water quality and to
understand the factors that affect it, thus addressing the questions:
|
The purpose of this report is to
describe what has been and will be done
in the second cycle of the NAWQA Pro-
gram in the San Joaquin–Tulare Basins
study unit. Results from the first cycle
are summarized in Dubrovsky and others
(1998). -
Introduction to the San Joaquin–
Tulare Basins study
The San Joaquin–Tulare Basins study
unit (fig. 1) is approximately 31,200
square miles; it includes the San Joa-
quin Valley, the eastern slope of the
Coast Ranges, and the western slope of
the Sierra Nevada. The Sierra Nevada
is predominantly forested land, and the
Coast Ranges and the foothills of the
Sierra Nevada are predominantly range-
land. Most of the valley floor is used for
agriculture. About 10 percent of the total
value of agricultural production in the
United States comes from California,
with the San Joaquin Valley produc-
ing about half of the California total.
Changes in water quality in the San Joa-
quin–Tulare Basins are primarily due to
the large amount of irrigated agriculture,
which affects the quality of both surface
and ground water in the Valley (Gronberg
and others, 1998).
Activities of Second Cycle
As part of the second cycle of
NAWQA assessments in the San
Joaquin–Tulare Basins, efforts will focus
on five major activities:
1. Status assessment of mercury.
2. Status assessment of ground-water
drinking water sources.
3. Assessment of water-quality trends
in streams and ground water.
4. Topical study of transport of anthro-
pogenic and natural contaminants to
community supply wells.
5. Topical study of agricultural chemi-
cals: Sources, transport, and fate.
125 years of science for America
* * * * *
1879–2004
U.S. Department of the Interior
U.S. Geological Survey
63 Printed on recycled paper
Fact Sheet 2004–3012
April 2004



121° Consumnes River
at Michigan Bar 120° CALIFORNIA
San Joaquin
sº Sacramento-
San Joaquin
Delta
San Joaquin River
near Vernalis 119°
near Crows Landing Nº.
8 Y NZ
& N. V.
º
EXPLANATION
VALLEY DEPOSITS
Basin deposits
| | Alluvial fan deposits
STATUS ASSESSMENT SITES
o Ground-water drinking
water assessment site o
118
V Mercury assessment site
36°
TREND ASSESSMENT SITES
V. Surface-water site
Major aquifer study site
Vineyard land-use site
..se/
W.W
§
Bakersfield
O
©
& Almond land-use site
© Corn-alfalfa-vegetable land-use site
BOUNDARIES OF TOPICAL STUDY AREAS
Agricultural chemicals: sources,
transport, and fate
Transport of anthropogenic o
<> and natural contaminants to 35
community supply wells 0 20 40 MILES
H
0 20 40 KILOMETERS
Figure 1. Locations of data collection sites for the second cycle studies of the San Joaquin–Tulare Basins, California.















status and ſends )
Status Assessment of Mercury
Mercury is one of the most widespread
contaminants affecting our Nation’s aquatic
ecosystems. Fish consumption is the
predominant route of exposure to methyl-
mercury for humans and wildlife. Mercury
sampling during the first cycle of NAWQA
was limited to analyses of total mercury in
fish livers and in Streambed sediment.
The San Joaquin–Tulare Basins study
unit participated in the NAWQA-wide
mercury assessment in the Summer of
2002, which involved analysis of water,
bed sediment, and fish for methyl and total
mercury at eight sites in the study area
(fig. 1). Data from this assessment will be
used by the mercury topical study to deter-
mine the occurrence and distribution of
mercury in diverse environmental settings.
These data will be used to contribute to a
better understanding of the bioaccumula-
tion of mercury in target game fish species
and of mercury cycling in streams.
Status Assessment of Ground-Water
Drinking Water Sources
Data analysis from the first cycle and
cooperative projects with other agen-
cies indicated the importance of assess-
ing drinking water sources in selected
locations as part of the NAWQA design.
This entails sampling for contaminants
in ground water that is directly used as a
source of drinking water.
In the fall of 2002, Source water from
15 community water-supply wells in the
Modesto urban area were sampled and ana-
lyzed for major inorganics, organic carbon,
trace elements, pesticides, volatile organic
compounds (VOCs), isotopes for age
dating, and selected microbes. Additional
samples will be collected from the commu-
nity water-supply wells during 2004.
Assessment of Water-Ouality Trends
The primary goal of the trend compo-
nent is to systematically assess long-term
trends in the chemical and physical quality
of the Nation's streams and ground water
and in the ecological condition of the
Nation's streams, and to relate observed
trends and changes to probable causes.
Streams
Four surface-water sites, each repre-
Senting a different part of the surface-
Water System, are being sampled as part
of the NAWQA trends network: San Joa-
quin River near Vernalis, Merced River at
River Road, Orestimba Creek near Crows
Landing, and Cosumnes River at Michi-
gan Bar (fig. 1). All except the Cosumnes
River have been sampled since the begin-
ning of the first cycle.
The San Joaquin River receives water
from tributaries draining the Sierra
Nevada and Coast Ranges, and except
for streams discharging directly to the
Sacramento–San Joaquin Delta, is the
only surface-water outlet from the study
area (about 31,200 square miles). The
water quality of the San Joaquin River
is of critical interest because it flows to
the delta. Both the Delta-Mendota Canal,
which supplies irrigation water to farms
in the western San Joaquin Valley, and
the California Aqueduct, which supplies
drinking water to Southern California,
originate in the delta.
The Merced River is located in a large
basin (about 1,383 square miles) on the
east side of the San Joaquin Basin. A
large reservoir in the basin stores clean
water from the Sierra Nevada; water
released from this reservoir is used for
agriculture and hydropower, and to assist
the migration of salmon and steelhead.
Streamflow below the reservoir is supple-
mented by storm runoff in the winter and
irrigation return flows during the Spring
and summer. About 56 percent of the
basin below the reservoir is agricultural,
thus, water quality of the Merced River
is a valuable indicator of the impacts of
agriculture on water quality in east side
tributaries to the San Joaquin River.
Orestimba Creek is an ephemeral
stream in a small agricultural basin (10.8
square miles) within the valley floor on
the west side of the San Joaquin Basin.
Streamflow results from Storm runoff in
the winter, and irrigation return flows
in the spring and summer. During the
winter, the creek can also receive runoff
from the Coast Ranges, depending on
the intensity and duration of storms, thus
increasing the drainage area to 195 Square
miles. Orestimba Creek is representative
of the Small western tributaries to the San
Joaquin River.
The Cosumnes River is in the northern
part of the study area and drains directly
to the Sacramento–San Joaquin Delta.
The basin is about 536 square miles. The
Cosumnes is essentially the last sig-
nificant free-flowing river from the Sierra
Nevada, with only minor regulation by
a small upstream reservoir. Past mining
activities in the Cosumnes River Basin
occurred upstream but within the basin. The
Cosumnes River is sampled upstream of
most of the agricultural activity in the basin,
and therefore is representative of a “refer-
ence” for unaffected water quality.
High-intensity sampling for the second
cycle of NAWQA started in October
2001; sampling frequency ranged from
every 2 weeks to monthly. In October
2003, Sampling frequency was reduced to
low-intensity sampling (8 to 9 times per
year). Water samples are being analyzed
for nitrogen and phosphorus nutrient spe-
cies, major anions, pesticides, and Sus-
pended sediment. The assessment of the
streams for ecological conditions include
the collection of fish, benthic inverte-
brates, and algae and the characterization
of instream and riparian habitat. The
ecological assessments are done annually
during the late Summer.
Ground Water
Wells used in a major aquifer study
(of the San Joaquin–Tulare Basins) and
in three agricultural land-use studies
conducted in the first cycle are being
resampled as part of the ground-water
trends assessment for the second cycle.
The area of the major aquifer study is
defined by the extent of the eastern allu-
vial fans physiographic region, which has
been intensively farmed and irrigated since
the early 1900s. The large quantity offer-
tilizers and pesticides used in this area, the
intense irrigation, and the generally perme-
able sediments have resulted in a history
of ground-water contamination problems.
Most of the population and ground-water
use in the San Joaquin–Tulare Basins is in
the eastern alluvial fans region.
The vineyard, almond, and corn—
alfalfa-vegetable land-use study areas
are nested within the major aquifer study
area. Vineyards and almonds continue
to be valuable and dominant crops in the
study area, ranking Second and tenth,
respectively, in total production and value
in 2001 in the State. The corn—alfalfa–
Vegetable land-use group encompasses
a large variety of crops and therefore a
large variety of pesticide applications.
Thirty wells from each study were
sampled in 2001 or 2002. These wells
will continue to be sampled on a decadal
Schedule. A Subset of wells from each
study will be sampled biennially to evalu-
ate the temporal trends within the decadal
sampling period. The subset of wells Sam-
pled biennially will be sampled seasonally
from fall of 2003 to Summer of 2004 to
determine how much the water quality var-
ies seasonally in these study areas.

Understanding-Topical Studies
Topical Study of Transport of
Anthropogenic and Natural Contaminants
to Community Supply Wells
Data analysis from the first cycle and
cooperative projects with other agen-
cies indicate the importance of assess-
ing drinking water sources as part of
NAWQA. The Transport of Anthropo-
genic and Natural Contaminants to Com-
munity Supply Wells study is addressing
the question, “What are the primary man-
made and natural contaminant sources,
aquifer processes, and well characteristics
that control the transport and transforma-
tion of contaminants along flow paths to
community supply wells in representative
water-supply aquifers?”
The San Joaquin–Tulare Basins is one
of eight areas across the Nation currently
involved in this process-oriented study.
The area of focus of this study is the val-
ley floor around and including the city of
Modesto (fig. 2). The specific objectives
of the study are to:
1. Characterize the regional hydro-
geologic setting and determine the
dominant ground-water flow paths
to community supply wells.
2. Evaluate dominant sources of
contaminants contributing to com-
munity Supply wells, including
agricultural and urban contaminants,
and geologic source areas for natu-
ral contaminants.
3. Develop an understanding of trans-
port and transformation processes
that affect anthropogenic and natural
contaminants as they are transported
to community Supply wells.
Results from the status assessment
of the sources of ground-water drink-
ing water, the first cycle investigations,
and other retrospective analyses are
being evaluated in relation to sources of
anthropogenic and natural contaminants.
The pesticide database maintained by the
State of California will be accessed for
information on pesticide applications.
Ancillary information such as geology,
land-use, and census data, data on leaky
underground fuel tanks, and data from the
National Uranium Resource Evaluation
Program will also be examined as surro-
gates for other chemical applications.
A regional ground-water flow model
extending from just north of the Stan-
islaus River to South of the Merced River,
west past the San Joaquin River, and east
to the edge of the alluvial fans was devel-
oped to help characterize the regional
flow system and determine the dominant
ground-water flow paths to the commu-
nity supply wells (fig. 2).
º
ſº º
Stockton -
37° 45' –
37° 30' –
37° 15' E-
Merced **
= | f Ground-water
_º A 2- 2 - Flow path
5 10 MILES -
120° 30'
º EXPLANATION
Basin deposits
| | Alluvial fan deposits
Study area for the
topical study of
transport of anthro-
pogenic and
natural contami-
nants to community
supply wells and
regional ground-
water flow study
---
. Ground-water flow
*TT and transport study
• Community supply
5 10 KILOMETERS
- well sampled
Figure 2. Study area for the topical study of transport of anthropogenic and natural contaminants
to community supply wells in and around Modesto, California.
Using the information from the
regional model and from the results of
an evaluation of possible contaminants,
a network of about 20 monitoring wells,
located along flow paths and beneath
Selected sources of contaminants, will
be installed between July 2003 and May
2004 (fig. 3). Continuous samples of
the subsurface material are collected at
selected intervals for solid-phase analy-
sis and aquifer sediment characteristics.
These wells will be sampled for a broad
range of constituents (including age dat-
ing) to provide information on the areal
distribution of contaminants in the local
study area. Ground-water levels will be
monitored in all wells; some wells will be
instrumented with continuous measure-
ment equipment.
A ground-water flow and transport
model, encompassing a part of the urban
Modesto area, will be developed (fig. 2).
The model will be used to evaluate the
relative importance of physical and chem-
ical processes that affect the contami-
nants moving along dominant ground-
water flow paths. Since the Modesto
area is typical of urban areas in the San
Joaquin Valley, this work can be useful
for extrapolation to other urban areas.
Figure 3. Drilling a monitoring well in Modesto,
California.







Topical Study of Agricultural Chemicals:
Sources, Transport, and Fate
Agricultural land use has a large
influence on the quality of Surface- and
ground-water in the United States. This
topical study addresses the questions,
“How do environmental processes and
agricultural practices interact to affect the
transport and fate of agricultural chemi-
cals in the hydrologic system of nation-
ally important agricultural settings, and
what are the effects on water quality and
implications for management of water
resources?”
The San Joaquin–Tulare Basins is one
of five areas across the Nation currently
involved in this study. The study area is
the Merced River Basin, located on the
east side of the San Joaquin River (fig.
1). This basin is predominately agricul-
tural in the valley floor part of the basin.
Within the Merced River Basin, two areas
will be studied intensively from 2003 to
2005: a ground-water flow path from an
agricultural setting that terminates in the
Merced River and the Mustang Creek
subbasin (fig. 4). The objectives of the
study are to:
1. Develop an annual mass budget
for water and selected agricultural
chemicals in the components of the
hydrologic system.
2. Determine the residence times
and rates of water and agricultural
chemical transport among the com-
ponents of the hydrologic system.
3. Identify the important chemical
transformation and transfer pro-
cesses for selected agricultural
chemicals.
4. Use quantitative methods for inter-
preting, extrapolating, and predict-
ing the fate and transport of water
and selected agricultural chemicals,
which can be applied to similar agri-
cultural settings at a range of scales.
5. Interpret study results as to the
implications for managing the water
and water-quality impacts of agri-
cultural systems.
Data on crop type and management
practices, such as water-, pesticide-, and
0 05 MILES
0 0.5 KILOMETERS
120°20'
0 10 MILES
0 10 KILOMETERS
EXPLANATION
| ] Study area for the topical
study of agricultural
chemicals: sources,
transport and fate
| Mustang Creek Subbasin
V Surface-water quality
and flow site
V Overland flow site
() Meteorological site
O Ground-water flow
path site
= Surface-water/ground-
water interaction site
O Unsaturated zone site
Figure 4. Study area for the topical study of agricultural chemicals: sources, transport,
and fate of the Merced River Basin, California.
fertilizer-use, will be collected for the
study area. The study can be catego-
rized into three broad components of the
hydrologic system: atmospheric, surface
water, and ground water.
Two precipitation sites within the
Mustang Creek Subbasin are being
sampled for targeted pesticides and their
transformation products. A third site is
being established on the ground-water
flow path near the Merced River. These
data, in combination with spatial meteo-
rological data, will be used to calculate
the areal distribution of chemicals to the
watershed via rainfall.
Surface-water sites along Mustang
Creek and a site near the mouth of the
Merced River will be sampled and ana-
lyzed for nutrients, pesticides, suspended
sediment, and other selected water-qual-
ity constituents. The Mustang Creek
subbasin is being modeled to simulate
surface-water flow. An overland flow site
will characterize runoff from a specific
field. Dye studies are being conducted
during the rainy season to determine
travel times along Mustang Creek.
The primary goal of the surface-water
assessments will be to identify temporal
patterns in the concentrations of selected
pesticides and nutrients and to relate
these patterns to surface-water transport
processes.
Activities relating to ground water
are being focused on characterizing the
movement of water and chemicals from
the land surface through the unsaturated
and Saturated zones to surface water.
Movement of water and chemicals
through the unsaturated zone (between
the land surface and the water table) will
be estimated by measuring irrigation and
evapotranspiration rates and by collecting
subsurface water samples using lysim-
eters. These data will be used to develop
simulations of unsaturated flow and
chemical transformations to generate a
better understanding of these processes at
the local scale.



Movement of water and chemicals
through the aquifer system beneath the
water table will be inferred using water-
level measurements and water samples
(for chemical and age-dating analyses)
collected from several multi-depth moni-
toring wells installed along the general
direction of ground-water flow toward the
Merced River. These data will be used to
calibrate a local-scale ground-water flow
model. This local-scale model will utilize
the results of the regional model devel-
oped for the topical studies.
Movement of ground water and
chemicals into the Merced River will be
inferred using a variety of data collection
(fig. 5) and analysis techniques. Vertical
hydraulic gradients will be determined
using water-level measurements in multi-
depth monitoring wells within the river
and riparian zone. Seepage rates and
chemistry will be determined at several
locations using seepage meters. Seepage
rates and hydraulic characteristics of the
riverbed will be determined using tem-
perature measurements and simulations
of heat transport.
Chemical sampling from monitoring
wells along the ground-water flow path
will include field parameters, pesticides,
nutrients, major ions, and dissolved
organic carbon. Selected samples at the
surface-water/ground-water interaction
sites will be age dated. At these sites,
sediment core samples will also be
collected and analyzed for bulk density,
particle size, percentage of organic
matter, soil moisture, selected minerals,
chloride, and nitrate. Denitrification rates
will be assessed by injecting nitrate and
a tracer into the riverbed and sampling
periodically, noting the rate of nitrate
disappearance.
The goal of this topical study is to
estimate the flux of water and agricultural
chemicals through the unsaturated zone,
into the Saturated zone, and between
surface water and ground water, and to
assess the chemical transformations that
occur as the water moves through these
different components of the hydrologic
System.
Figure 5. U.S. Geological Survey scientists showing techniques used to measure (A) direction of
ground-water flow; (B) temperature below streambed; and (C) stream discharge.
References Cited
Dubrovsky, N.M., Kratzer, C.R., Brown,
L.R., Gronberg, J.M., and Burow,
K.R., 1998, Water Quality in the San
Joaquin–Tulare Basins, California,
1992–1995: U.S. Geological Survey
Circular 1159, 38 p.
Gilliom, R.J., Hamilton, P.A., and Miller,
T.L., 2001, The National Water-Quality
Assessment Program—Entering a new
decade of investigations: U.S. Geologi-
cal Survey Fact Sheet 071-01, 6 p.
Gronberg, J.M., Dubrovsky, N.M.,
Kratzer, C.R., Domagalski, J.L.,
Brown, L.R., and Burow, K.R., 1998,
Environmental setting of the San Joa-
quin–Tulare Basins, California: U.S.
Geological Survey Water-Resources
Investigations Report 97-4205, 45 p.
Hirsch, R.M., Alley, W.M., and Wilber,
W.G., 1988, Concepts for a National
Water-Quality Assessment Program:
U.S. Geological Survey Circular 1021,
42 p.
by Jo Ann M. Gronberg, Charles R. Kratzer,
Karen R. Burow, Joseph L. Domagalski,
and Steven P. Phillips
For more information contact:
U.S. Geological Survey
Placer Hall, 6000 J Street
Sacramento, California 95819
Telephone: (916) 278-3000
Home page: http://ca.water.usgs.gov/sanj/
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