The Aquifer of the San Joaquin Valley

Stephanie Trump

Where the San Joaquin Valley?

The Central Valley aquifer system is located in a large structural trough in Central California. The aquifer system is divided into three subregions on the basis of surface water basins.

The San Joaquin Valley Aquifer is located in central California in the counties of San Joaquin, Stanislaus, Merced, Madera, Fresno, Tulare, Kings, and Kerns. It is part of the larger Central Valley Aquifer System. The Central Valley Aquifer System also includes the Sacramento Valley Aquifer and the Sacramento-San Joaquin Delta Aquifer. The Central Valley aquifer system, of which the San Joaquin Valley aquifer is a part, is a structural trough about 400 miles long and twenty to seventy miles wide and covers more than 20,000 square miles.

So, where does the aquifer get its water?

Before development, most of the recharge to the Central Valley aquifer system was from rain and snowmelt in the mountains at the valley margins, and discharge was to rivers and marshes near the valley axis.

Before development began, the aquifer system was under steady-state conditions in which natural recharge balanced natural discharge. Ground water in the shallow part of the aquifer system flowed from areas of high altitude at the valley margins, where most of the recharge took place, downgradient to discharge into rivers and marshes near the valley axis. This pattern changed after the area became heavily settled. Due to heavy pumping, water in the confined parts of the aquifer move toward the areas where water is being withdrawn.

Under unstressed, predevelopement conditions, ground water in the upper part of the Central Valley aquifer sytem flowed from up-land recharge areas at the valley margins to discharge areas, such as rivers, lakes, and marshes on the valley floor.

The aquifer system is recharged naturally by streams coming from the Coast and Cascade Ranges on the western side and the Sierra Nevada Mountains on the east of the valley. Most of the natural recharge is in the northern and eastern parts of the valley. Recharge from precipitation is very small, mostly because this area does not receive much rainfall. Most natural recharge occurs at the edges of the Central Valley, and the ground water moves in the subsurface to lower altitudes and discharges into surface-water bodies, such as lakes and rivers, that drain each basin. Most recharge of the aquifer comes from percolation of irrigation water and the efforts of people. One example of recharge through the efforts of people is Leaky Acres. Leaky Acres is operated by the city of Fresno. It consists of twenty-six groundwater recharge ponds on 200 acres. It was built in 1970 to store water with the intent of using the water to artificially recharge the aquifer.

Nearly all the recharge received by the Central Valley aquifer system is provided by runoff from the mountains that surround the Central Valley. http://gwatlas/valley/intro.html

What kinds of rocks and soils are found in the aquifer?

The Central Valley is a large structural trough that has been partially filled by marine sediments and continental deposits. The Sierra Nevada, which forms most of the eastern boundary of the valley, is the edge of a huge tilted granite block. The Coast Ranges, which form most of the western boundary, consist, for the most part, of folded and faulted marine rocks.

The San Joaquin Valley is a large area, and the soils and rocks vary. On the eastern side, the soils come from the Sierra Nevada. They mostly consist of highly permeable, medium to coarse-grained sands. Soils on the western side of the valley come from the coast ranges and have a higher clay content and finer texture than on the eastern side. In the center part of the San Joaquin Valley near the rivers, Holocene stream deposits of coarse sand, gravel, and silt are present. Away from the rivers, flood basin deposits, which are moderately to densely compacted clays, are found. There are also areas near Fresno and around the Merced River. These sands are fined-grained and well-sorted. The San Joaquin Valley also contains marine sediments, a result of being covered by the ocean at times during the past. The Central Valley is surrounded and underlain with consolidated volcanic and metamorphic rocks. These rocks are almost impermeable. The aquifer is heterogeneous.

The hydraulic conductivity can be seen on the graph below. This aquifer is rather large and has a variety of specific yields for different areas. For example, the specific yield for the Turlock Subbasin is 10.1 percent, and the specific yield in the Kaweah Subbasin is 10.8%. The San Joaquin Valley contains two aquifers: an upper unconfined to semi-confined aquifer, and a deeper, confined aquifer. These two are separated by a clay layer, known as “blue clay,” “Corcoran Clay,” or “E-clay.” The clay is a member of the Tulare Formation and is of Pleistocene age. It is a lacustrine deposit and has very low permeability, and ranges in thickness from twenty feet to more than 100 feet. Clays and other fined-grained materials make up about 50% of the aquifer system. The thickness of the semi-confined zone ranges from 400 feet near the valley trough to more than 800 feet at the foot of the mountain range. The thickness of the aquifer ranges from less than 500 feet to over 4000 feet.

The thickness of the Central Valley aquifer system that is saturated with freshwater is greatest in the San Joaquin Valley, where freshwater extends to a depth of more than 4,000 feet below the land surface.

For what purposes is this water being used?

The primary use of groundwater in this area is agriculture, but with a growing population, the water is being used for urban water supplies. Currently, seven million acres are being irrigated. The invention of the deep-well turbine pump around 1930 allowed water to be pumped from greater depths. During the early years of ground-water development in the coastal basins, from the 1850's to early 1900's, the principal use of water was for irrigated agriculture. Although agricultural ground-water use remains substantial, urbanization has gradually replaced most agricultural land in the larger basins and the greatest collective ground-water demand is now for public supply. The largest water users are cities and suburbs from San Francisco southward, but because of the unequal distribution of rainfall, most of the freshwater is in northern California. Accordingly, it has become necessary to regulate streamflow and import water into many coastal basins from the Sierra Nevada, the Colorado River, the Owens Valley, and northern California through an extensive system of aqueducts.

Agricultural irrigation is by far the major ground-water use in the Central Valley (A). More ground water is withdrawn in the Tulare Basin than elsewhere (B), because that basin is the driest area of th valley.

Are there any threats to this aquifer?

The large amounts of groundwater pumped have caused subsidence. Most of the subsidence has been caused by three processes; oxidation and compaction of peat, hydrocompaction, and compaction of fine-grained sediments due to withdrawal of ground water in excess of recharge. Of these three, the last process has caused the most widespread and severe subsidence.

Land subsidence has affected large areas of the Central Valley. Most of the subsidence is the result of compaction of fine-grained sediments, which has been caused by large withdrawals of ground water.

When an aquifer has been severely overdrafted, it will never again be able to hold its pre-overdraft amount. There is some storage loss that is not permmanent. The storage capacity in coarse-grained materials can be regained. Subsidence due to compaction of fine-grained sediments began in the San Joaquin Valley in the 1920's. Approximately one-half of the valley, or about 5200 square miles, had subsided at least 1 foot by 1977. In 1977, a drought year, withdrawals reached a maximum of 15 million acre-feet.

As a result of increased surface-water importation during the 1960's and 1970's, ground-water withdrawals were reduced and water levels rose in the deep confined aquifer in many areas from 1961 to 1976. However, declines continued in the southern part of the San Joaquin Valley.

Since the 1970's, steps are being taken to minimize further subsidence. Each year, through seansonal precipitation, artificial recharge, and irrigation replenish aboout 85-90% of the groundwater being pumped.

The most serious threat to this aquifer is nonpoint source (NPS) contamination from chemicals used in fertilizers and other products used in the agricultural industry. NPS contaminants are widely distributed, may be persistent, may be toxic below the detection limit, and are routinely applied in modern farming practices. Of these chemicals, atrazine has been the most frequently detected parent compound in national water quality sampling studies., and the second most common pesticide found in drinking water welles. Atrazine's high potential for ground water contamination is the result of a low tendency for sorption in combination with a comparatively long half-life. There are alson other things monitered in this area. These include: Salinity, boron, and selenium. Salinity and boron affect agriculture, and selenium affects wildlife. High salinity is often the result of the mixing of pristine groundwater with descending evaporative brines formed in Buena Vista Lake. It can also occur when groundwater becomes mixed with with oil field brines that infiltrate into the groundwater from unlined sump pits. Brine is also injected into the aquifer by shallow, oil field disposal wells. Cation exchange at depth tends to concetrate sodium at the expense of calcium. Pesticide or fertilizer contamination raises nitrate levels.

Althoug hte quality of the water in the Central Valley aquifer system in generally suitable for agricultural, industrial, and public-supply uses, some areas have potential or actual problems. Boron levels thatare damagine to some crops are in ground water in the Sacramento and the San Joaquin Valleys; nitrate levels that might be damaging to crops or that exceed drinking-water standards are in the Sacramento Valley; selenium levels that exceed drinking-water standards are in trhee wells in the Sacramento Valley; potentially toxic levels of heavy metals are in the western part of the San Joaquin Valley; and the pesticide dibromochioropropane has been detected throughout the San Joaquin Valley.


  • USGS. Groundwater altas of the United States. Central Valley
  • San Joaquin Geological Society
  • SJVDIP and University of California Ad Hoc Coordination Committee.