IV.E WATER RESOURCES AND QUALITY
E. WATER RESOURCES AND QUALITY
1. INTRODUCTION
Water resources in San Joaquin County include rivers, streams, sloughs, marshes, wetlands,
channels, harbors, and underground aquifers. The extensive Delta Basin waterway system is one of
San Joaquin County's most valuable water resources. Over 700,000 acres of agricultural land and 700
miles of interlacing waterways form the Sacramento-San Joaquin Delta. Four rivers, numerous creeks,
and various bodies of water are partially or entirely within the County. The San Joaquin River and its
tributaries threading their way through the Delta provide an unusual area of refreshing beauty and
sustain many wildlife varieties of commercial and recreational importance. The largest striped bass
spawning grounds along the Pacific Coast are located in the Delta. The Stockton Deep Water
Channel through the Delta and the San Joaquin River is used as a navigational channel by large
commercial ships which stop at the Port of Stockton. The various waterways in the County are used
extensively for boating, water-skiing, swimming, hunting, and fishing (an estimated 3 million angler
days per year in the Delta).
The County receives its water supply from both underground and surface water. A rapidly expanding
population and ensuing economic development are increasing pressures on the County's present
water supply. At the same time, water quality is being threatened by commercial and domestic wastes,
agricultural discharges, and recreational uses. Locally, water quality maintenance is under the
jurisdiction of the San Joaquin County Department of Public Health Services, and at the State level,
under the Regional Water Quality Control Board. Groundwater overdraft is causing salt water intrusion
and subsidence in some areas.
Management policies governing the approximately 370 miles of rivers and sloughs will be critical in
determining the County's character, its pattern of future growth and quality of life. The county
maintains a Water Policy Statement to assist in establishing water management policies. The Water
Policy Statement is developed by the Advisory Water Commission which serves in an advisory
capacity to the Board of Supervisors. This appendix describes the existing water resources,
addressing issues of water quality, uses, and current and future sources of supply.
2. HYDROLOGY
Water in San Joaquin County comes from both groundwater aquifers and surface water supplies.
Average rainfall ranges from 8 inches per year south of Tracy to 17 inches per year in Lodi. The mean
annual precipitation for Stockton is 14.3 inches. Most of the precipitation occurs between December
and April, with the summer months virtually rainless. Therefore, groundwater supplies must be
recharged and surface water must be retained to supply year-round needs. Most of the rivers entering
the County have been impounded; reservoirs generally provide both flood control and a steady supply
of water, for which a multitude of agencies negotiate. Table IV.E-1 contains a description of the
surface and groundwater resources of the County and their beneficial uses.
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WATER RESOURCES AND QUALITY (cont.)
3. SURFACE WATER
Rivers and Streams. The major rivers which enter the County from the Sierra Nevada are the San
Joaquin, the Mokelumne, the Calaveras, and the Stanislaus (see Figure IV.E-1). The San Joaquin
originates in Fresno County, crosses southwestern San Joaquin County and empties through the Delta
into Suisun Bay. The other rivers join the San Joaquin at or near the Delta. The Mokelumne
originates in Alpine County, crossing the northern portion of the County and forming the County line
close to the Delta. The Calaveras, which originates in Calaveras County, crosses the central County.
The southern boundary of the County is formed by the Stanislaus, which originates in Alpine County.
Several small, generally intermittent streams join these rivers or discharge into the Delta.1
Water Supply. All of the major rivers in the County have been modified by impoundments or diversion
channels. The Pardee Reservoir on the Mokelumne River supplies water to the East Bay Municipal
Utility District (in the San Francisco Bay Area), and the Camanche Reservoir on the Mokelumne River
supplies water to the North San Joaquin Irrigation District. The New Hogan Reservoir on the
Calaveras River supplies water to the Stockton East Water District. The Stanislaus River, with New
Melones Reservoir, is a source of future water supply. Stockton East Water District is proposing to use
New Melones water by diverting water via canal to the Calaveras River.
The San Joaquin River drains the northern San Joaquin Valley. It serves as a transportation route for
ships to pass from the San Francisco Bay to the inland Port of Stockton. A deep water shipping
channel is maintained for this purpose. The river also is used for irrigation by adjacent farmers.
Two aqueducts on the west side of the County carry water from the Delta to Southern California.
These aqueducts also supply water locally. The California Aqueduct, operated by the California
Department of Water Resources, supplies water locally to Musco Olive and Tracy Golf and Country
Club. The Delta-Mendota Canal, operated by the U.S. Bureau of Reclamation, serves the City of
Tracy as well as several irrigation districts and individuals.*1 Properties along the rivers also exercise
riparian water rights.
At the present time only the cities of Stockton and Tracy use surface water for municipal supplies, although they also pump from the groundwater supply. The Stockton East Water District has built a
water treatment plant in southeast Stockton to treat surface water for domestic use. Water from New
Hogan Reservoir supplies the plant. The City of Tracy also constructed a water treatment plant in
1979, processing water from the Delta-Mendota Canal.
Further details on water supply in San Joaquin County can be found in the Utilities Chapter of this
Document.
*1
These include the Plainview Water District, Banta-Carbona Irrigation District, West Stanislaus Irrigation District,
West Side Irrigation District, Hospital Water District, Teichert Construction and the Arnaudo Brothers.
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TABLE IV.E-1: WATER RESOURCES AND THEIR BENEFICIAL USES IN SAN JOAQUIN COUNTY
Beneficial Uses
Water Resources
A
San Joaquin River
Mokelumne River
B
Storage
Capacity
(AcreFeet)
C
D
E
X
X
X
X
X
X
Other
Operating Agency
X
X
--
--
N/A
Riparian farmers,
Shipping industry,
Irrigation Districts
--
--
--
125,000
Irrigation Districts
431,500
N/A
Local residents
Water Districts
1
X
Calaveras River
X
Stanislaus River
X
X
Delta
X
X
Delta-Mendota
Canal
X
X
X
X
U.S. Bureau of
Reclamation
California Aqueduct
X
X
X
X
California
Department of
Water Resources
X
Lodi Lake
1
2
3
X
X
X
X
X
X
Scenic
Users
Source of
Supply
--
Comanche
Reservoir (1963)
Ground Water
flood control
Annual
Water Use
(Acre-Feet)
EBMUD
Mokelumne
River
--
--
--
--
--
--
--
318,051
--
Multiple Sources
--
N/A
Recreationists, Wildlife, USBR ,
3
DWR , shipping industry
Sacramento
River
N/A
144,205
City of Tracy, Irrigation Districts,
Commercial, Businesses
Sacramento
River
N/A
N/A
--
Mokelumne
River
N/A
--
--
San Joaquin
Valley Ground
Water Basin
570,000,000 9,300,000
(1972 pumpage)
Irrigation Districts
2
Commercial, Businesses,
Irrigation Districts
Local residents
Private individuals, cities, towns
East Bay Municipal Utility District
U.S. Bureau of Reclamation
California Department of Water Resources
N/A Not Available
Source: San Joaquin County, Department of Planning and Building Inspection, water resource surveys, July 1986; California Waters Atlas, 1979; interview with EBMUD,
U.S. Bureau of Reclamation, San Joaquin County Flood Control Engineer; Stockton -East Water District.
Key:
A = Irrigation
B = Municipal/Industrial
C = Recreation
D = Transportation
E = Estuary/Wildlife Area
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WATER RESOURCES AND QUALITY (cont.)
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WATER RESOURCES AND QUALITY (cont.)
4. GROUNDWATER
In 1980, groundwater accounted for approximately 30% of the water supplies in the County.2 The
most useful aquifers underlie the upland valley. Very little is found in the foothills of the Sierra Nevada,
although some alluvial fans contain a small amount. Groundwater is replenished by rainfall and
percolation of surface and irrigation water. Some areas of the County allow more recharge than
others. Buildings, pavement, or other impermeable surfaces decrease the area available for water
penetration. In the Stockton area, the groundwater supplies have been used faster than they have
been replaced, causing saline waters to infiltrate freshwater supplies.
Recharge Requirements. The County conducted a study in 1985 to determine the extent of the
groundwater problem.3 This study found that east of the Delta, the groundwater levels declined an
average of 1.7 feet per year between 1947 and 1984, for a total drawdown of 64.6 feet. This overdraft
caused the saltwater intrusion, which advanced eastward approximately one mile between 1963 and
1983. A groundwater model developed by the study team indicated that if no additional surface water
is available for groundwater recharge, water levels will fall as much as 160 feet below sea level and the
saline front will move eastward an additional two miles by the year 2020. Continued overdraft could
result in subsidence, which would diminish the recharge capabilities of the basin and create or
exacerbate flood hazards.
Recharge, or replenishment of groundwater aquifers, is necessary to correct problems caused by
groundwater overdraft. A large amount of recharge occurs in upland valley areas, especially adjacent
to rivers and larger streams. A small amount occurs in alluvial fans at the base of the foothills. Figure IV.E-2 shows the recharge areas in San Joaquin County. These areas must be protected so that
further recharge can occur. Any development which would result in paving over a substantial recharge
area or discharges of polluting wastes could seriously jeopardize the County's future water supply.
To restore groundwater levels, it is estimated that approximately 220,000 acre-feet of supplemental
surface water would be needed per year. This water could come from New Melones Reservoir,
Folsom South Canal, or in the short term from the Calaveras River. The Folsom South Canal, a
diversion from the American River, has been proposed to be extended further south from its present
terminus at the Rancho Seco nuclear power plant in Sacramento County. The canal would supply the
eastern side of San Joaquin County. If the canal is not constructed, other sources would be needed.
A multi-faceted water program and coordination between all agencies which provide water are
necessary to ensure the continued availability of water in the future. The County also needs to work
closely with the agencies bringing in supplemental water. The County is hiring a water coordinator to
bring all the programs together.
Regardless of what is done to bring supplemental water into the County, conservation and monitoring
are necessary. Individual wells and some urban areas are not currently metered. Monitoring of
pumping from the groundwater is necessary to prevent further reduction in the groundwater levels.
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WATER RESOURCES AND QUALITY (cont.)
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5. UNIQUE WATER RESOURCES
Sacramento-San Joaquin Delta. The Delta is an 1,100 square-mile region of levees, islands, and
interconnected waterways located at the confluence of the Sacramento-San Joaquin Rivers. This vast
area covers five counties and nine cities, bounded on the east by Interstate 5, on the west by the
Sacramento River, on the north by the City of Sacramento, and on the south by Old River. Significant
natural resource areas in the Delta are described in the technical appendix on "Vegetation, Fish, and
Wildlife Habitat." Surrounding the Delta are major population centers of the San Francisco Bay Area,
Sacramento, and Stockton.
The construction of the levees over the past 100-plus years has created 700,000 acres of reclaimed
marshland devoted primarily to agriculture and farming. It is one of the richest agricultural areas in the
nation. The peat soils produce over $375 million in crops annually.4
The Delta's 700 miles of interconnected waterways is one of the largest bodies of protected water in
the western United States. The Delta waterways provide for a vast range of recreational activities
which include boating, fishing, swimming, waterskiing, picnicking, and sightseeing. Over 7 million
visitors spend an estimated $73 million on Delta recreation annually, supporting another important
sector of the County's economic base.5 Despite the extensive reclamation and recreational use, the
Delta still provides important fish and wildlife habitat. It is a resting point on the Pacific Flyway, which is
a major migratory route for birds from all of North America, including areas as far north as the
Canadian Arctic. The Delta requires deliveries of fresh water to help repel saltwater intrusion and to
maintain its significant and nationally important wildlife habitat and fishery. In all, the Delta wetlands
support 225 species of resident and migratory birds. The waterways also contain 44 species of
commercial and sport fish. The number of some species are dwindling as a result of deteriorating
water quality and reverse flows drawn to the state water pumps.
Freshwater Marsh. Freshwater marshes occur in low-lying areas and along rivers and lakes. As an
ecosystem, a marsh supports a variety of plant and animal life and serves several functions including
flood control, enhanced water quality, groundwater recharge, fish nursery, biological productivity, and
wildlife habitat.
Marshes are also cultural amenities which provide natural scenery, scientific and educational
opportunities, and recreation, such as hunting or nature study. Resident animals and birds found in
San Joaquin marshes include the marsh hawk, Virginia rail, great blue heron, mallard, muskrat, and
beaver. Cattail, tule, sedges, and rushes are plants commonly found in the marshes.
6. IRRIGATION AND DRAINAGE
Agricultural activities demand a significant portion of the County's water supply. Most crops require
summer water. About 30% of the irrigation water comes from groundwater; the rest is from surface
supplies. Irrigation water can either be pumped into "spud" ditches adjacent to crops, sprinkled, or
delivered by drip irrigation. Of the three, ditch irrigation is most wasteful of water, but it is a simple
system to manage. Drip irrigation systems are expensive to install and maintain, but they make the
most efficient use of water.
Excess water applied to crops, as well as stormwater, result in runoff. Some may percolate through
the soil below root zones and help to recharge groundwater aquifers. However, in areas of
impermeable soils, the soils can become waterlogged or excessively saline for crops. Soils in San
Joaquin County west of the San Joaquin River have some drainage problems. Tile drains have been
installed; however, there are no provisions for disposal of accumulated salts. Treatment of drainage
water, especially agricultural runoff, demands attention.
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WATER RESOURCES AND QUALITY (cont.)
Endnotes
1. San Joaquin County Council Governments. San Joaquin County Agricultural Land Preservation
Study. June 1980.
2. California Department of Water Resources. Groundwater Basins in California. Bulletin 118-80.
January 1980.
3. Palilla, Marco and Salo, John. "Surface Water the Answer in San Joaquin Basin" in Brown and
Caldwell Quarterly. October 1985.
4. California Department of Water Resources. Delta Outdoor Recreation Implementation Plan.
Prepared by Applied Research Consultants. June 1981.
5. California Department of Water Resources. Delta Recreation Concept Plan. Prepared by Geidel
and Moore. January 1981.
References
1. Water Conservation News: Over Irrigations Not Recommended for Discharge, February 1984.
2. American Farmland Trust. Eroding Choices, Emerging Issues. San Francisco, CA. 1986.
3. Brown and Caldwell. Eastern San Joaquin County Groundwater Study. October 1985.
4. California Department of Water Resources. Ground Water and Environment - San Joaquin
County, proposal for the Cities and County of San Joaquin Advisory Planning Association. June
1972.
5. Herb Matzinger, California Department of Water Resources. Personal communication. July 8,
1986.
6. John Lind, Tracy Office, U.S. Bureau of Reclamation. Personal communication. July 8, 1986.
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