The Sacramento-San Joaquin River Delta of California once was a great tidal freshwater marsh blanketed
by peat and peaty alluvium. Beginning in the late 1800s, levees were built along the stream channels,
and the land thus protected from flooding was drained, cleared, and planted.
Although the Delta is now an exceptionally rich agricultural area, its unique value is as a source of
freshwater for the rest of the State. It is the heart of a massive north-to-south waterdelivery system.
Much of this water is pumped southward for use in the San Joaquin Valley and elsewhere in central and
The leveed tracts and islands help to protect water-export facilities in the
southern Delta from saltwater intrusion by displacing water and maintaining favorable freshwater
gradients. However, ongoing subsidence behind the levees reduces levee stability and, thus,
threatens to degrade water quality in the massive north-to-south water-transfer system.
History of Development in the Delta Area
The Delta, located at the confluence of the Sacramento and San Joaquin Rivers, is blanketed by peat and
peaty alluvium deposited where streams, originating in the Sierra Nevada, Coast Ranges, and southern
Cascade Range, enter the San Francisco Bay system. In the late-1800s, large-scale agricultural development
in the Delta required levee-building to prevent frequent flooding. The leveed marshland tracts then had
to be drained, cleared of wetland vegetation, and tilled. Levees and drainage systems were largely
complete by 1930 and the Delta had taken on its current appearance, with most of its 1,150-square-mile
area reclaimed for agricultural use (Thompson, 1957).
Today the Delta includes about 57 islands or tracts that are imperfectly protected from flooding by
more than 1,100 miles of levees. Reclamation and agriculture have led to subsidence of the land surface
on the developed islands in the central and western Delta at long-term average rates of 1-3 inches per
year (Rojstaczer and others, 1991; Rojstaczer and Deverel, 1993). Many of the islands in the central Delta
are presently 10 to nearly 25 feet (ft) below sea level. As subsidence progresses, the levees themselves
must be regularly maintained and periodically raised and strengthened to support the increasing
stresses on their banks. Currently, the levees are maintained to a standard cross section at a height
of 1 ft above the estimated 100-year flood elevation.
An extensive network of drainage ditches prevents islands from flooding internally and maintains
groundwater levels deep enough for agricultural crops to grow. The accumulated agricultural drainage is
pumped through or over the levees into stream channels. Without this drainage, the islands would become
The dominant cause of land subsidence in the Delta is decomposition of organic carbon in the peat soils.
Prior to agricultural development, the soil was waterlogged and anaerobic (oxygen-poor). Organic carbon
accumulated faster than it could decompose. Drainage for agriculture led to aerobic (oxygen-rich) conditions
that favor rapid microbial oxidation of the carbon in the peat soil. Most of the carbon loss is emitted
as carbon dioxide gas to the atmosphere (Deverel and Rojstaczer, 1996).
The Delta as a Source of Fresh Water
The Delta receives runoff from about 40 percent of the land area of California and about 50 percent of
California's total streamflow. It is the heart of a massive north-to-south water-delivery system whose
giant engineered arterials transport water southward. State and Federal contracts provide for export of
up to 7.5 million acre-feet per year from two huge pumping stations in the southern Delta near the
Clifton Court Forebay (California Department of Water Resources, 1993). About 83 percent of this water
is used for agriculture and the remainder for various urban uses in central and southern California.
Two-thirds of California's population (more than 20 million people) gets at least part of its
drinking water from the Delta (Delta Protection Commission, 1995).
Tidal Action and Water Salinity
The waterways of the Delta are subject to tidal action. Ocean tides propagating into San Francisco Bay
are observed 5-6 hours later along the Cosumnes River in the eastern Delta. The position of the interface
between the saline waters of the Bay and the freshwaters of the Delta depends upon the tidal cycle and
the flow of freshwater through the Delta.
Before major dams were built on rivers in the Delta watershed,
the salinity interface migrated as far upstream as Courtland along the Sacramento River (California
Department of Water Resources, 1993). Today, releases of freshwater from dams far upstream help reduce
the maximum landward migration of the salinity interface during the late summer. In the spring, however,
reservoirs and Delta exports consistently act in concert to increase the landward migration of the
salinity interface over that expected under conditions of unimpaired flows1 (Knowles, 2000).
Land subsidence of Delta islands indirectly affects the north-to-south watertransfer system, which is
predicated on the available water supply (annual inflows to the Delta), the viability of aquatic
species populations, and acceptable water quality in the southern Delta. The presence of the western Delta
islands, in particular, is believed to effectively inhibit the inland migration of the salinity interface
between the Bay and Delta.
If these islands were to become permanently inundated with saline water, the
water available to the massive pumping facilities near the Clifton Court Forebay might become too
saline to use. The timing of levee breaks and flooding is critical in this regard.
Fortunately, most flooding occurs in winter and spring, when major saltwater intrusion is less likely.
However, there are occasional levee failures under low-flow conditions. These failures can cause major
short-term water-quality problems, even if the flooded areas are later reclaimed. During one such
incident, an island was flooded under low-flow conditions, and chloride levels reached 440 parts
per million (ppm) at the Contra Costa Canal intake, which is well above the California standard for
drinking water of 250 ppm (California Department of Water Resources, 1995).
The leveed tracts and islands help to protect water-export facilities in the southern Delta
from saltwater intrusion by displacing water and maintaining the salinity balance.
Two Subsidence Threats
The statewide water-transfer system in California is so interdependent that decreased water quality in
the Delta, whether due to droughts or levee failures, might lead to accelerated subsidence in areas
dependent on imported water from the Delta. How might this happen? Many areas of central and southern
California that are dependent on Delta water also are susceptible to another kind of subsidence.
Historically, over-pumping in the San Joaquin and Santa Clara Valleys compacted critically stressed
aquifer systems, resulting in land subsidence (Galloway and others, 1999). Before imported Delta water
became available in the mid-1970s, nearly 30 ft of subsidence had been measured in the San Joaquin Valley
and up to 14 ft in the city of San Jose in the Santa Clara Valley. Estimated damages were in the hundreds
of millions of dollars, largely due to costs associated with construction of flood control structures and
well damage. Both the Santa Clara and San Joaquin Valleys now rely, in part, on imported water from the
Delta to augment local supplies and, thereby, reduce local ground-water pumpage and arrest, or slow,
subsidence. Degradation of the Delta source water could lead to increased ground-water use and
renewed subsidence in these and other areas in California.
The Sacramento-San Joaquin Delta|
The heart of California's water systems
An artificial balance is maintained in the water exchanged between the Delta and the San Francisco Bay.
Freshwater inflows regulated by upstream dams and diversions supply water to the Delta ecosystems and to
farms and cities in central and southern California.
Subsidence of Delta islands threatens the stability of island levees and the quality of Delta water. Delta
levee failures would tip the water exchange balance in favor of more saltwater intrusion, which can ruin
the water for agriculture and domestic uses. Several aqueducts would be affected. Any reductions in the
supply of imported Delta water could force water purveyors in many parts of the State to meet water demand
with ground-water supplies. This, in turn, could renew land subsidence in the Santa Clara and San Joaquin
Valleys and exacerbate subsidence in Antelope Valley and other areas that currently are reliant on
imported Delta water supplies and prone to aquifer-system compaction.
Annual Inflow (red): An amount equivalent to about 25 percent of the Delta's inflow is pumped into California's
massive water system. Some of the rest is used locally, but most flows into the San Francisco Bay.
Annual Outflow (orange): The Delta receives runoff from about 40 percent of the land area of California and
about 50 percent of California's total streamflow.
Salinity: Salinity intrusions are linked to the interactions of tides, watermanagement programs, and
climatic variability. When freshwater flows decrease, higher salinity water can move into the Delta. On average,
upstream control structures, such as Folsom, Shasta, and Oroville Dams, have reduced the extent of salinity
intrusions by providing freshwater releases during the summer and fall. However, from February through
early June the reservoirs effectively remove water from Delta outflow. The peak effect of this removal
tends to occur in May as reservoirs in the southern Sierra capture snowmelt runoff (Knowles, 2000).
This makes the Delta more susceptible to salinity intrusions in the spring.
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| Map of the Sacramento-San Joaquin River Delta area showing land subsidence in feet below sea level. Image by USGS.
|Cross-sections through delta "islands" showing the predevelopment natural levees and the postdevelopment constructed levees. Image by USGS.
|Field studies (Deverel and Rojstaczer, 1996) determined that the increased flux of carbon dioxide gas from the drained peat soils was sufficient to explain most of the carbon loss and measured subsidence. The dissolved organic carbon pumped from the islands in agricultural drainage could account for only about 1 percent of the carbon loss. The studies also showed that rates of carbon-dioxide production increase with increasing temperature and decrease with increasing soil moisture.
|The statewide water-transfer system in California is so interdependent that subsidence in the Delta might lead to accelerated subsidence in areas dependent on imported water from the Delta.
Challenges in the Delta's Future
Delta-island subsidence caused by peat oxidation only can be controlled by major changes in land-use
practices. The continuation of agriculture in the Delta depends on a sufficient peat thickness. In
much of the cultivated area of the Delta, substantial thicknesses of peat remain so that there is great
potential for further subsidence.
The Delta currently is the subject of a major Federal-State-stakeholder effort (called CALFED) to develop
a long-term plan to restore ecological health and to improve water management of the Bay- Delta system.
This plan includes restoring wetland and riparian habitat along the outside of the levees and on several
of the smaller, less subsided islands. Presently, there are no planned restoration activities in the heavily
subsided areas within the central Delta islands. Much of the extensively subsided area is impractical to restore
and will continue to require some monitoring and, perhaps, maintenance. As subsidence progresses, the levee system
will become increasingly vulnerable to catastrophic failure during floods and earthquakes. The interrelated issues
of Delta land subsidence, water quality, and wildlife habitat will continue to pose a major dilemma for California's water managers.
Possible long-term management strategies for various Delta islands include:
1. Shallow flooding to mitigate subsidence by slowing peat oxidation and allowing growth of wetland vegetation that contributes biomass accumulation.
2. Shallow flooding combined with thin-layer mineral deposition (a possibly beneficial reuse of dredge material).
3. Continued use of agricultural areas with shallow peat and (or) low organic-matter content, under the assumption that the additional subsidence will not destabilize the levees.
4. Addition of thick layers of mineral soil, possibly using controlled levee breaches or deposition of dredge material, to slow peat oxidation and raise land-surface elevation.
5. Deep flooding to create freshwater reservoirs.
These strategies may be implemented in a mosaic throughout the Delta
that creates a substantial diversity of wildlife habitat-uplands, open
water, shallow permanent wetlands, and seasonal wetlands.
California Department of Water Resources, 1993, Sacramento-
San Joaquin Delta atlas: California Department
of Water Resources, 121 p.
California Department of Water Resources, 1995, Delta levees: California Department of
Water Resources, 19 p.
Delta Protection Commission, 1995, Land use and
resource management plan for the primary zone of the
Delta: Delta Protection Commission, 60 p.
Deverel, S.J., and Rojstaczer, S.A., 1996, Subsidence of
agricultural lands in the Sacramento-San Joaquin Delta,
California. Role of aqueous and gaseous carbon fluxes:
Water Resources Research, v. 32, p. 2,359-2,367.
Galloway, D.C., Jones, D.R., and Ingebritsen, S.E.,
1999, Land subsidence in the United States: U.S. Geological
Survey Circular 1182, 177 p.
Knowles, Noah, 2000, Natural and human influences
on freshwater flows and salinity in the San Francisco
Bay-Delta estuary and watershed: Interagency Ecological
Program for the Sacramento-San Joaquin
Estuary Newsletter, v. 13, no. 1, p. 5-23.
Rojstaczer, S.A., and Deverel, S.J., 1993, Time dependence
of atmospheric carbon inputs from drainage of
organic soils: Geophysical Research Letters, v. 20, p.
Rojstaczer, S.A., Hamon, R.E., Deverel, S.J., and
Massey, C.A., 1991, Evaluation of selected data to
assess the causes of subsidence in the Sacramento-
San Joaquin Delta, California: U.S. Geological Survey
Open-File Report 91-193, 16 p.
Thompson, John, 1957, The settlement geography
of the Sacramento-San Joaquin Delta, California:
Palo Alto, Calif., Stanford University, Ph.D. dissertation,
For additional information contact:
U.S. Geological Survey
Placer Hall, 6000 J Street
Sacramento, CA 95819
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