Delta Subsidence in California
 

The sinking heart of the State
 

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 (over a $500 million 

crop value in 1993), 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 water

delivery system. Much of this water is pumped southward for use in the 

San Joaquin Valley and elsewhere in central and southern California. 

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.

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-squaremile 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 longterm 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-yearflood elevation.

An extensive network of drainage 

ditches prevents 

islands from flooding internally and 

maintains groundwater levels deep 

(California Department of Water Resources)

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 flooded. 

-

Rio Vista

Courtland

Stockton

Antioch

Sa n Joa quin

River

Sacramento

Rive r

Levee

0 to10

10 to15

Greater than 15

Land subsidence,

in feet below sea level

Clifton Court

Forebay

To 

San 

Francisco

Bay Sherman Island

Chipps

Island

Tyler I.

Grand I.

California Aqueduct

(State operated)

Tracy Pumping Plant

South Bay

Pumping Plant

Delta-Mendota Canal

(Federal operated)

Contra Costa Canal

South Bay

Aqueduct

0 5 Mi

0 5 Km

Harvey O. Banks

Delta Pumping Plant

Cosumnes R.

N

CALIFORNIA

Map area

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 

US Department of the Interior FS-005-00
 

US Geological Survey April 2000
 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

of the carbon loss is emitted as carbondioxide gas to the atmosphere (Deverel 

and Rojstaczer, 1996).

The Delta’s unique value as a 

source of freshwater

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 usesin 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).

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

 

 

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.

Main channel Channel

Natural levees were formed

by sediments deposited 

during spring floods 

and stabilized by

vegetation.

“Tule” (bulrush

and reed species) Water table

Peat soils were formed

from decaying vegetation

over thousands of years.

Riparian vegetation was 

cleared and levees were

built to create farmland. Semicontinuous pumps 

remove agricultural 

drainage to maintain

a low water table.

Levees must be periodically

raised and reinforced to

support increasing stresses 

from stream channels.

Saucer-shaped profile reflects greatest thickness 

and subsidence of peat

soils near the center of

the islands.

Not to scale

PREDEVELOPMENT

POSTDEVELOPMENT 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.

the Bay and the

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.

In flooded conditions,

 decaying tules decom-

 pose slowly to release 

 carbon dioxide (CO2) 

 and methane (CH4). 

Exposure to air accelerates 

the decay of tules and peat

 soil. Organic material is

 converted mainly to CO2

 and water.

ANAEROBIC CONDITIONS: Oxygen poor AEROBIC CONDITIONS: Oxygen rich

Oxygen (O2)

Carbon

dioxide (CO2)

Carbon

As peat soils

decompose, the 

land “vaporizes” 

and subsides.

1Unimpaired flows refer to the hypothetical flows that would occur in the estuary without water storage 

diversions and exports, upstream and in the Delta, but in the presence of the existing channels and levees. 

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 mil-
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

lion (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 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.

TheTyler Island levee was breached in a 1986

flood. Such levee failures have been common in

the Sacramento-San Joaquin Delta since reclamation began in the 1850s. Each of the islands and

tracts in the Delta has flooded at least once, with

several flooding repeatedly. About 100 levee failures have occurred since the early 1890s. Initially,

most of the failures were caused by overtopping

during periods of spring flooding. Although construction of upstream reservoirs since the 1940s

has reduced the threat of overtopping, it has not

reduced the incidence of levee failure.

(California Department of Water Resources)

The Sacramento-San Joaquin Delta: The heart of California’s water systems

Sacramento River

(21.2 maf)

San Francisco Bay

(21 maf)

Contra Costa Canal

(0.1 maf)

Consumptive use/

channel depletion

(1.7 maf)

South Bay and

California Aqueducts

(2.5 maf)

Delta-Mendota Canal

(2.5 maf)

East side streams (1.4 maf)

Precipitation

(1 maf)

San Joaquin River (4.3 maf)

San Francisco Bay

Pacific Ocean

BEFORE UPSTREAM

DAMS BUILT

Maximum salinity

instrusions,

1921 to 1943 

AFTER UPSTREAM

DAMS BUILT

Maximum salinity

instrusions,

1944 to 1990 

Wet

year

Dry

year

Wet

year

Dry

year

An artificial balance is maintained Annual Outflow1 Annual inflow

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 waterexchange 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. 

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.

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 sus1 ceptible to salinity intrusions in the spring. Flow data from 1980–1991

(California Department of Water Resources 1993)

(Note: maf,millions of acre feet)

N
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Reclamation—draining

Delta islands

Ground-water pumpage increases

regional land subsidence

Subsidence of islands

Levee instability

Increased water salinity

Reduced water exports

Sacramento-San Joaquin Delta

San Joaquin

Valley

Santa Clara

Valley

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.

The future of the Delta 

poses many challenges

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 BayDelta 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.

—S.E. Ingebritsen, Marti E. Ikehara, 

Devin L. Galloway, and David R. Jones

FUTURE STRATEGIES

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.

REFERENCES

California Department of Water Resources, 1993, Sacramento-San Joaquin Delta atlas: California Department of Water Resources, 121 p.

———, 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. 

1,383–1,386.

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 SacramentoSan 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, 551 p.

For additional information contact:

Kimberly Taylor

U.S. Geological Survey

Placer Hall, 6000 J Street

Sacramento, CA 95819

(916) 278-3264

ktaylor@usgs.gov

Helpful internet sites:

http://sfbay.wr.usgs.gov

http://calfed.ca.gov